Furumori from Dragon Crisis!. He was angry at the society because, when he was a researcher there, a female researcher he was working with was afflicted with a cursed precious treasure. He wanted to get a lost precious from one of the higher ups, but they constantly refused, which caused her to die. As a result, he went rogue and kidnapped/raised a girl to help him steal lost precious in order to share it with the world. Unfortunately, he didn't care how he got it and who had to get hurt or die in the process (although, in the anime at least, they never show him or Ai, his "dog", actually killing anyone, although he does try to do that to Ryuuji).
Neon Genesis Evangelion: SEELE's leaders want to eliminate sorrow in the world...through a murder and manipulation galore. Gendo wants to reunite with his dead wife and not cause his son pain...which causes him to be a jerkass of a father and a cruel manipulator of a lover.
Almost the entire cast of Code Geass. In fact, it's probably the point of the series.
Magnificent Bastard and Villain Protagonist Lelouch is actually a well-intentioned extremist. His primary goal is overthrowing the oppressive Social Darwinistempire because it tramples on those who are weak or kind-hearted. Oh, and there's lots of mass murder of its third-class citizens and anyone who lives in a country that it wants to take over. In a subversion, even he has trouble stomaching some of the steps it takes to achieve his goal, as seen when he becomes physically sick after killing a half-brother who fully supported the empire - and more than that, killed several thousand people to keep his illegal experiments hidden - and nearly breaks down after unintentionally causing the death of his beloved half-sister who was much nicer and dedicated to similar but less extreme goals. In all, it was a choice between a terrible, terrible thing, and an even more terrible thing. Except for the Euphemia thing. He was, with a little prodding, willing to give up rather than oppose her. Or shoot himself, it's a little unclear.
Then the show really messes with the audience when it reveals that both of Lelouch's parents, Emperor Charles (whom he despises) and Marianne (whom he admires) intended on creating an ideal world free of war, strife, or lies, by slaying the gods and starting their own version of Ragnarok. Oh, and they ask him to go along with it too. Though it's likely that the plan wouldn't have worked anyway, due to certain things in the first season.
Lelouch throws the "Well-Intentioned" out of Extremist when he becomes a despotic overlord and Emperor of the world, and moves to execute any and all political opponents. Oh, wait, no, that's how he wants to portray himself, so that once the world's hate is concentrated on him, he can arrange for himself to be publicly assassinated, ending the chain of hatred by setting up the infrastructures and political status quos he had set up earlier himself and achieve world peace through his feigned death, symbolically killing the world's hatred with him.
Schneizel had his own designs for bringing about world peace. They just happened to involve nuking a bunch of key cities and using the Black Knights as pawns.
Even Nunnally, ofallpeople, becomes one when she mixes parts of both Lelouch's and Schneizel's strategies for world peace to concoct her own, somewhat less drastic, scenario. She had indisputably good intentions, but the plan still involves threats, nukes, social engineering, and effective world-domination. It most definitely runs in the family.
To her defense, she didn't planned to use nukes, but she just couldn't stop Schneizel. So her plan was to get along with him and, when opportunity arrived, to get rid of him and Damocles, which would become symbol of hate.
And then there is Kallen, who is, without a doubt, the most straightforwardly heroic character in the series, but that didn't stop her from seriously considering stabbing Shirley to death for almost blowing her cover. Not to mention her mecha's face meltingly devastating signature attack. Yeah, the whole series is filed to the brim with this trope.
PLANT Chairman Gilbert Durandal in Gundam SEED Destiny, inspired by Rau Le Creuset's inability to understand his own existence (which drove him insane and allowed him to nearly wipe out the human race), decides that human conflict stems from their dissatisfaction of their own roles and abilities, and attempts to implement an utopian society through the Destiny Plan, which would craft a world civilization under genetic determinism. To this end, he is perfectly willing to manipulate the masses, assassinate his political opponents, destroy countries, and use superweapons, all while maintaining an extremely high level of charisma.
Durandal also believes that uniting the world will prevent future Le Creusets from having any real success. After all, if there's only one nation, there won't be different factions for people like Rau to set against one another.
To his credit, his goals also included the elimination of LOGOS, a military-industrial complex that was perpetuating War for Fun and Profit (mostly profit, since they owned most/all of the mobile suit manufacturers).
And another Gundam example, Zechs Merquise/Milliardo Peacecraft of Gundam Wing, who became convinced, in the final episodes of the anime, that the only way to end humanity's penchant for war was to destroy the Earth, the cradle of humanity's bloody history, as he believed that the people of the space colonies were purer in purpose in regard to peace than those who lived on Earth.
More than that, though, it was an idea hatched by Zechs and Treize to show humanity a conflict so bloody and violent that humanity would lose the will to fight ever again. It's sort of like an intentionally planned World War I, and actually ends with the same results: mainly, that people DO lose the will to fight...for a while.
Both of them were inspired by Char Aznable (Durandal even has the same Seiyuu) from the first Mobile Suit Gundam series, or, to be more precise, Char's Counterattack, in which Char tries to make the Earth uninhabitable to force the population to migrate into space, which he believes will prevent wars by making everyone a Newtype.
And G Gundam has Master Asia, Domon Kasshu's Old Master. When he's first revealed as a villain, he seems to be just another brainwashed minion of the Devil Gundam, but he eventually reveals that he's Not Brainwashed and is aiding the Devil Gundam of his own free will. From his time on Earth in the previous Gundam Fight, Master Asia concluded that humans were destroying the planet. The Devil Gundam had been made (as the Ultimate Gundam) to restore the Earth with its nanomachines, but, due to a malfunction, it concluded that this mission required it to Kill All Humans. Master Asia agreed. When Domon finally defeats Master Asia near the end of the series, Master sees the error of his ways. But, of course, Redemption Equals Death.
Let's not forget Gundam 00s Celestial Being. The whole point of their actions is to beat up/kill any human factions who wish to wage war against each other.
They get better about this as the story progresses, and become much more selective in their targets. They even ally with an anti-government military force in the second season. Their overall goal of eliminating conflict through force remains, though.
All of it was a Xanatos Gambit by Schenberg to unite humanity in order to prepare them against an Alien Invasion.
All Ryoko Asakura from Suzumiya Haruhi wants to do is to break the status quo and incite some reaction from the titular character. Her method happens to be trying to murder the narrator, and major love interest, Kyon. When she returns in the tenth novel as a Boxed Crook, she still wants to kill Kyon because she still believes that her actions were justified. Still, she protects him, because she wants to be the one to kill him.
Also, both Tachibana Kyouko and Fujiwara, in the Anti-SOS Brigade, qualify as well, though the latter is more of a Knight Templar. Kyouko wants to protect the universe from destruction, and so believes that Sasaki, rather than Haruhi, is the best person to have godlike powers, since Sasaki has no desire to reshape the world. She says that she has no ill will against Kyon, but disagrees with the SOS Brigade's philosophy. Fujiwara, on the other hand, believes that the existence of Stable Time Loops in this series prevent any possibility of free will, so he wants to prevent the discovery of time travel, thus changing history and proving that free will exists. Unfortunately, he will stop at nothing to achieve this goal, including the attempted murder of children.
Celestin from Ah! My GoddessThe Movie is, in tune with the emphasis on romance in the series, a much lighter version of this. Still, the fact that he purposely erases Belldandy's memory of her love for Keichi specifically, infects her with a virus that uses her as a contact point to infect Yggdrassil, and forces her to undergo a procedure that has a 16% chance of working properly, otherwise erasing all of Bell's memories of not only Keichi but her sisters and Heaven itself, all in order to gain the power necessary to eliminate sadness and suffering from the world by force shows that he's not exactly nice either.
The Anti-Spirals from Tengen Toppa Gurren Lagann are out there to prevent the universe from being destroyed by an overload of Spiral Power, and in order to do that, they take The Heartless way and prevent any feelings of hope and courage from sprouting around the Universe.
Rossiu from the same arc of the same series qualifies, as he betrays his friend Simon by placing the blame for the Anti-Spiral attacks on him, sets him up in a phony trial, and sentences him to death so he can stop the riots. He realizes that the only way to save any part of humanity is to let a majority of them die. There's no other option, he tells himself. After Simon escapes custody and saves the day (and the world), Rossiu remembers what genre he's living in and decides to take his own life, but Simon forgives him and shows him the light. And by "the light", I mean a clenched fist moving slightly below the speed of sound followed by a pep-talk. Gotta love that little guy.
Ironically, he actually commented on this himself a while earlier:
Rossiu: Sometimes the best intentions can lead us down the wrong path.
Similarly, Lord Genome. To protect humanity from growing too numerous and being wiped out, he forced it underground and had the Beastmen kill anyone who wandered onto the surface.
Finally, at least from the viewpoint of the three above, Simon himself and the Dai Gurren-Dan, who are doing exactly what the antagonists fear will destroy humanity/the Earth/the universe, and with no other justification than "Who the hell do you think we are?" Some of them come around by the end, though.
Light Yagami from Death Note started out like this: he wanted to use the Death Note to rid society of its worst scum. However, his massive ego combined with so much power gave him a god complex that would soon lead him to jump off the slippery slope into true villainy.
Makubex of Get Backers is a great example of this trope. He's introduced as the villain of the I.L. story arc with the goal of creating an atomic bomb to use as a bargaining chip for the God of Infinity Fortress, in order to say 'stop controlling us or else'. Of course, trying to make a deal with God by using an atomic bomb may not be the best METHOD of madness, but, at heart, his goals are to make life better for the enslaved masses of Infinity Fortress' Lower Town, which has become a living Hell since Ginji left.
In Space Runaway Ideon, the Buff Clan's supreme military leader, Doba Ajiba, was willing to risk the destruction of the majority of his race if it meant the destruction of the Ideon. Of course, when one considers that the power of the Ide was forcing the Earthlings and Buff Clan to genocidally slaughter each other, it probably is the lesser of two evils.
Not to mention that the home planets of both the Earthlings and the Buff Clan were just destroyed by meteors, leaving those fighting as the few left of their kind.
The villain of the third Tenchi Muyo! OVA, Z, becomes one due to unfortunate circumstances.
Nagi from Mai-Otome believes that the Otome system of sending female bodyguards off to war in place of their country's leaders is an outdated model, and wants to put an end to it (which is exactly what series protagonist Arika wants to do)...by literally destroying the system from which the Meisters derive their abilities, using ancient weaponry and a horde of sentient monsters (summoned by cultists willing to give up their lives for the cause).
Itachi Uchiha in Naruto. Kill your entire clan, including your mother, father, and best friend for peace? Mind Rape your brother into becoming an "avenger"? Sympathetic Good or Stupid Evil? You decide, but he did get a Freudian Excuse.
Also, Pain, whose goal is to eliminate war. His plan involves collecting all of the Tailed Beasts (killing their human containers in the process) to make a weapon of mass destruction that will kill millions and scare all of the countries into not fighting for a while before fighting inevitably returns, at which point, one side will get hold of and use this weapon again, giving rise to another short time of "peace". Small periods of peace is his goal, which shows that he has a better grasp of human nature than Watchmen's Extremist.
Human nature perhaps, but international relations? No. He fails that forever.
Danzo also qualifies. His ultimate goal, much like Naruto and Pain, is to bring about peace in the ninja world. However, he believes that this can only be done through power, to the exclusion of hindrances like emotion. He's not above brainwashing people or attempting to subjugate all other ninja villages, even if that requires the deaths of countless people, to achieve his goals.
Subverted, however, with Madara, who, at one point, says that he is doing all these horrible things because he wants peace. Naruto sees through the lie and accuses Madara of not giving a shit about peace and only wanting power. Madara agrees. Since he's not really Madara, that might have been a lie.
The British Library in R.O.D the TV honestly believes that the world will be a better place if Mr. Gentleman rewrites everyone's memories and personalities however he pleases, including their own. Strangely, they never think to ask him if he thinks it's a good idea...
To Aru Majutsu no Index: Aureolus Izzard, who isolated himself three years ago after failing to save Index from having to have her memories erased and has been desperately trying to find a cure ever since.
Several magic side characters fall under this, especially under the Roman Catholic Church, and most especially, God's Right Seat, with most of them bordering on Knight Templar.
Also Accelerator, who tried at least to make the Sisters run away by talking in an aggressive way before each "experiment" starts.
However, the "Well Intentioned" part of the trope is very suspect when it comes to anyone involved in the Level 6 development projects. Other than reaping its benefits (and likely being used again later by its supervisors), Accelerator doesn't have any good intentions in his involvement with the Sisters experiment, or with anything, for that matter, at least, until Last Order shows up.
From the spin-off To Aru Kagaku No Railgun, Professor Kiyama Harumi, who developed the Level Upper as part of a scheme which ultimately led to the saving of a group of comatose children from a failed AIM diffusion experiment. What sets her apart is that, while her plan does involve putting at least ten thousand esper aspirants in comas, she prepared a cure beforehand and has the full intention of using it once she's done. She also tried more legitimate means first, but after nearly two dozen failures and the fact that the city's administration and law enforcement aren't going to budge, not least because of the whole Academy City conspiracy, she resorted to this.
In Hunter × Hunter, Meryem, the Chimeran Ant King, suddenly makes a dramatic change into becoming a Well-Intentioned Extremist from a Complete Monster who wants to Kill All Humans. After befriending a human girl (whom he originally kept alive so he could one day defeat in the only strategy game he wasn't prodigal at), he learns that there are certain humans that deserve to live, and remakes his plan for the Chimeran Ants inheriting the Earth. Instead, he decides to protect the weak and remake the world so that it is so equal, the word "equality" doesn't even exist anymore. The extremist part? He wants to abolish the old system by force, and is only willing to protect the weak that he deems "have the right to live."
Admiral Gil Graham from Magical Girl Lyrical Nanoha A's wanted to stop the Book of Darkness and its multi-dimensional destructive ways, even if it would cost the lives of the Wolkenritter and result in Hayate being sealed away with the book.
You can also make an argument about the Wolkenritter being this in order to save Hayate from the Book of Darkness's corruption by completing its pages as quickly as possible and having Hayate's wish granted.
From Magical Girl Lyrical Nanoha StrikerS, the TSAB high council, who are responsible for creating Scaglietti and letting him build combat cyborgs and artificial mages for them to ensure the safety of the TSAB controlled worlds.
Donan Cassim, the governor of the colony planet Deloya in Fang of the Sun Dougram, stages a fake coup d'état and uses it as an excuse to order a planet-wide hunt for dissidents and guerrillas, simply because he believes that the planet can only prosper as a part of the Earth Federation and that most Deloyans are opposed to independence anyway. He actually believes in making the colony prosper a bit too much to become the show's Big Bad, so he is later killed by his Evil Chancellor aide.
Elite Four Lance in Pokémon Special. He views humans as completely incompatible with Pokémon, so he plans to commit genocide against the human race so that Pokémon can live in peace and the world can return to its natural glory.
Maxie and Archie from the R/S arc had the same ambition in the manga as they did in the games. Of course, corruption by the Red and Blue Orbs drove them Bugfuck insane before all was said and done.
There's also Mewtwo from Pokémon: The First Movie. Enraged by humanity using Pokémon as tools and disgusted by the acceptance of this by the Pokémon, he sought to remake the world by exterminating everyone and replacing them with clones. This way, he thought, Pokémon would have the freedom they deserve.
Of course, Mewtwo didn't bother asking Pokémon just why they accepted humans as masters. It may seem cheesy, but friendship and trust are basically what make the Pokémon world even work. Just don't expect fanfiction to acknowledge this.
Uh, dude? Mewtwo hated the fact that CLONES were being mistreated, not just Pokemon in general. In fact, the first movie (at least, the original Japanese version) states that Mewtwo wanted to wage war not only against humanity, but against ALL natural-born life in general. Contrast that with Mew, who feels that clones (including Mewtwo) are inferior and must be destroyed.
Um... what? You mean Mew, the Friend to All Living Things adorable child who spends the entire movie doing nothing but poking around curiously at things and doesn't have any interest in fighting whatsoever until Mewtwo outright attacks it? Alternate Character Interpretation much?
No, he's right. In the original Japanese film, Mew told Mewtwo that clones (including Mewtwo) were inferior and should be destroyed - remember that part in the dub where Meowth translates for Mew, and Mew says some generic Power of Friendship stuff? Yeah, that's not what Mew said in the original...
Marcus, the Man Behind the Man in Pokémon Movie 12, wanted to preserve Miichina Town, something he believed would result in it reverting to a wasteland if the Jewel of Life was returned to Arceus. However, he ended up brainwashing Damos and forcing him to betray Arceus, and it was implied that he did the exact same to the other Pokemon.
The Big Bad of Movie 14 wanted to restore his civilization by reviving one of the two legendary pokemon (which one depends on which movie is viewed).
The entire cast of Mirai Nikki, no exceptions. Yes, even him. No Exceptions.
Hitomi in Code: Breaker. He just wants recognition for the scores of anonymous, mostly teenaged Code: Breakers who died in the line of duty by killing 50,000 people and the prime minister of Japan, whose estranged son is also a Code: Breaker. His goal is spat back in his face by his own protégé, who reminds him that all Code: Breakers are just superpowered murderers put to good use and that their anonymity is for the best.
From JoJo's Bizarre Adventure: Stone Ocean: the truly faithful Father Pucci, whose ultimate goal is to reach the "Heaven" he heard his mentor Dio talk about. He'll do anything and sacrifice anyone to get to it, and apparently, he does: he rewinds, remakes, and resurrects the world (that he completely messed up), but is killed before he can join it.
Kuze from Ghost in the Shell: Stand Alone Complex is a complete Anti-Villain and even all around likable. You kind of have to cheer him on once his motives become clear and you learn more about what he has accomplished so far. But arming terrorists with guns, attacking the prime minister with a katana, using kokaine as a weapon to damage the leadership of the countries he opposes, and building nuclear bombs to threaten his enemies puts him quite far in the deep end of extremist territory.
And there's, of course, Gouda, who tricked Kuze into doing all these things. If Japan wasn't willing to face all it's social issues, he would force them to deal with them.
Witch Hunter Robin: the characters discover that they're a part of this when the truth about the witch-proof substance, Orbo, is revealed (it's made of witches!).
Two of the major Filler villains in the Bleach anime fall under this trope, choosing to side with villains or adopt villainous powers and methods to bring about (what they feel) would be positive changes in Soul Society.
An interesting case is Princess Mononoke, as both sides of the conflict are led by Well Intentioned Extremists. The central plot of the film is Ashitaka's attempt to stop the unnecessary fighting.
Most of the villains from Getter Robo, curious for a classic Super Robot Genre series. The Dinosaur Empire was caught up in a war of species dominance, trying to stop their extinction, while Burai and the Andromeda Flow Country were committed to stopping the use of Getter Energy - the power of evolution - before it endangered the whole universe.
Burai followed the imperative to destroy Getter, imprinted into him by the Andromedian machinery that gave him power, but he also wanted to take over the Earth because he could.
Lucif from Venus Versus Virus sought the True World, which is some kind of Utopia without suffering.
The Koorime from Yu Yu Hakusho. They believe that, as long as there are no males living among them, they will survive and be peaceful, and they'll do anything to keep it that way, even if it means separating a baby from his mother and tossing him off a floating island miles high in the air.
Hell, Sensui was this even when he was a Spirit Detective. He considered all demons pure evil before his Face Heel Turn.
Yoki in Waq Waq, who wants to end the tyranny of the red-blooded humans over the black-blooded ones by sacrificing a red-blooded girl, then betraying the villains.
In Speed Grapher, the Big Bad Suitengu's life was ruined by greed, money, and corruption. His intention was to destroy these things. However, he had to become a monster in order to do it.
Many of the "villains" in Mahou Sensei Negima!, but especially Fate, who claims to be trying to save the inhabitants of the Magic World by erasing it from existence.Kurt Godel would probably count too, if we can ever confirm his ultimate goal, though he also claims to be trying to save the world by keeping Fate from destroying it.
Turns out, they both have very similar plans. The magical world's running out of energy, and when it goes, most of its 1.2 billion inhabitants will vanish, with 67 million being dumped onto an empty, airless Mars. Kurt wants to evacuate those 67 million before it's too late to save those that can be saved, whereas Fate realizes that it isn't fair to those that can't be evacuated, and Earth can't deal with 67 million refugees - so he'll just kidnap everyone and send them to a pocket dimension that is suspiciously afterlife-like.
The latter is kind of hilarious, when you stop to think about it. As of the most recent chapter, it seems like the Final Battle will boil down to who can save the world better.
One has to wonder if maybe Negi is the well intentioned extremist in this story. Chao went back in time to stop Negi from doing just what he is now trying to do, but Negi just keeps barrelling ahead with his plan. Although Your Mileage May Vary, seeing as how his plan includes information deduced from Chao's visit, so Chao either successfully prevented her Bad Future or made it happen.
Fate and his band also make a point of not harming anyone from Earth, except when Fate notices that Mahora will be collateral damage. But by that time, he has switched to full-on Blood Knight and no longer cares about anything else.
The eponymous Noein is suffering from grief from losing the love of his life, Haruka. He then searches for other dimensions where she might have survived, but finds that she's always destined to the same fate in every universe. His intention is then to converge all universes to stop all suffering, erase all existence and start it anew.
Yamaki in Digimon Tamers wants to destroy all Digimon, or, at the very least, every single one in the real world, good or not. He has a Heel Face Turn when he realizes that his efforts are actually helping Digimon get into the real world by damaging the barriers.
Mirroring this, Zhuqiaomon wants to destroy all humans and conquer the real world because he feels they endanger the Digimon's chances of defeating the D-Reaper. He also does a Heel Face Turn when Azulongmon convinces him that they should be focusing on defeating the D-Reaper instead.
X1999's Dragons of Earth seek to save the Earth from those destroying it — Humans — by eliminating them, and allowing the Earth to regrow and return to its natural state.
The three ruling students in Fly High control their school with an iron fist and won't allow anyone to start a student council because their friend, who didn't stand out physically or academically, was horribly bullied by the previous student president and stopped coming to class. At the end, they acknowledge that they've become the kind of people they wanted to stop.
Angela and the rest of the organization, too. They want to purify everyone...in a rather violent manner.
Rex Godwin in Yu-Gi-Oh 5Ds, who just wants to deal with the Signer conflict permanently by combining the powers of his brother's Signer Birthmark and his own Dark Signer Birthmark he picked up to overpower both gods and destroy the world to rebuild it anew so that the cycle doesn't start all over again in 5000 years' time.
All of Yliaster count as this, especially their mastermind, ZONE. His plan is to wipe out Neo-Domino and Momentum to prevent his Bad Future from happening again. The tool is his Arc Cradle, which he aims to use to destroy Neo-Domino and everything in the surrounding 30 miles, sacrificing millions of lives, all in a last effort to save not only billions, but the planet itself.
Yes but at the end of the Doma arc, it's revealed that Dartz was brainwashed by the Orichalcos so it wasn't exactly his fault.
In Supercar Gattiger, the Big Bad, Emperor Black Demon, wants to conquer the world so he can put an end to war.
Jellal Fernandes of Fairy Tail wanted to create a world where everyone could be free and no one would ever suffer. He decided to do this by attempting to ressurect Black Mage Zeref, the Ultimate Evil of the entire series, and using his power to achieve that goal. Laxus Dreyar is a more minor example. He wanted to make Fairy Tail a stronger guild, but his plan for doing so was to take it over by force and boot out everyone who didn't meet his ideal of a powerful mage.
While not so much evil as antagonistic, Haruka of the Mai-Hime manga has the goal of having her Ori-Hime unit deal be the only one entrusted with destroying the Orphans. To accomplish this and dispose of her Orphan Resistance rivals, she tries to have Nao lure Yuuichi away by seducing him, orders Akira to steal Mikoto's Element, and kidnaps Mikoto and Kazuya. When word of this gets out, her approval rating plummets, and Mai and Natsuki defeat her and Yukino, ending her plans and resulting in the two groups working together.
Takano Miyo, main villain of Higurashi No Naku Koro Ni, just wants her grandfather's work to be acknowledged. The way she does this? Killing the entire village of Hinamizawa
Kyubey in Puella Magi Madoka Magica can be seen this way: what it's trying to do is avert, or at least delay, the heat death of the universe. Doing this just happens to involve driving young girls over the Despair Event Horizon, since those emotions can be efficiently harvested as energy for that purpose. Kyubey doesn't see anything wrong with this: its species doesn't have emotions, and so does not understand human value systems. It even thinks that it's being unnecessarily nice in the way it goes about it, since it will only make a girl into a Puella Magi if she agrees to it (though Kyubey will rarely reveal all the details until after the agreement is made).
Ra's al-Ghul's intention in the Batman comics (and Batman The Animated Series) was to stop mankind's destruction of the environment. This could be accomplished by wiping out roughly 2 billion people. In the movie Batman Begins, he attempts to make Gotham an example of crime and decadence in order for the world to see its horror.
Bioterrorist Poison Ivy wants plants to be respected. It's the "and completely dominant" part that causes trouble.
Magneto in X-Men; a common comparison, implicit in the Live-Action Adaptation, is that Lensherr is the 'Malcolm X' to Charles Xavier's more moderate 'Dr. King'. Of course, Magneto goes much further than that.
Xavier himself can be quite unscrupulous. Danger and Vulcan are both consequences of his 'whatever it takes' attitude.
Exactly how sympathetic Magneto is in his goals varies from writer to writer, with him ranging from a sympathetic anti-villain to a borderline Complete Monster. The Chris Claremont version, which fits this trope the best, is simply the best-known.
There is even a stretch where Magneto serves as Headmaster, and genuinely seems to wish to aid the New Mutants and carry on Xavier's dream. However, this doesn't last.
Spider-Man's enemy, the Vulture, is a good example of the other type of this trope. Many years after his debut, he was given a backstory in which an unscrupulous business partner cheated him out of the proceeds from his inventions. He wrecked said partner's business, stole back his money, and discovered that he enjoyed the thrill. Eventually, the partner surfaced, and the usually not-murderous Vulture went after him; Spidey stopped the Vulture but taped the partner's confession.
Cinderella's fairy godmother, as well as Geppetto, in Fables embodies this trope. The fairy godmother just wanted people to be happy, and Geppetto didn't start out intending to conquer the world.
Grant Morrison's Marvel Boy is a good example of this. The miniseries' alien protagonist, the extradimensional Kree, Noh-Varr, has his ship shot down and the rest of his crew killed by a supervillain that wants to make a profit off of his technology and dissected remains. As such, he winds up understandably pissed at the human race (to the extent that he knocks down buildings to spell out "F#$k you" to the human race in letters several blocks high, though he herds the inhabitants away so there will be no casualties). Noh-Varr finds Earth's social ills to be ridiculous and unreasonable and intends to make war on Earth and "terraform" it to be like his home planet, Hala. He would be a classic Villain Protagonist, but genuinely does seem to believe that what he's doing will better Earth for its inhabitants.
Norman Osborn during the Dark Reign saga saw himself as this, as we see in his "monologue" at the end of Siege. He says that his idea was to make a safer world by not letting just anyone put on a costume and decide to save the world by themselves, since they would end up causing more harm than good, knowing that, someday, the mutants would turn against mankind, or the Hulk would snap and go on a rampage that could kill millions. And he used the Superhuman Registration Act in his attempt, since it would be the perfect excuse - whoever was against him was automatically labeled as "non-sanctioned" and hunted down.
Professor Fairfax in Paperinik New Adventures. The problem: as the years go on, overpopulation and dwindling natural resources will become more and more of a problem. The solution: using earthquake machines to raise a large section of the Pacific Plate above sea level, freeing up space for new cities and farms. Never mind that the ensuing earthquakes and floods will all but wiped out the entire west coast of the United States. As one character puts it: "If you think about it, his plan isn't illogical at all: he's simply willing to kill millions of people to give billions of people a better future."
Rayek in ElfQuest claims to want what's best for all of elfkind, but is also convinced that he's the only one who knows what's best for them, in spite of all arguments to the contrary. This comes to a head when, in an attempt to correct a Time Paradox, Rayek takes Leetah, Skywise, Ember, Suntop, and Picknose and his family ten thousand years into the future in the Palace - leaving Cutter and the rest of the Wolfriders stranded in the present.
Winowill starts out as one of these. She just wants to keep all the "real" elves nice and safe, even if it means keeping them locked in perpetual stasis and committing genocide on the Wolf Riders. Later, she just becomes plain out and out Ax Crazy evil.
The major turning point seems to be the time she drove her own son insane in order to cover up the murder of her troll lover. After that, there were no limits to what she'd stoop to.
Watchmen: A very spoilerish example, but: Ozymandias? Possibly the most successful Well Intentioned Extremist in fiction. He kills three million people to achieve world peace...and, as far as the reader can tell, it works, though the last panel opens up the possibility that it may have all been for nothing.
Another example would be Rorschach, whose violent and murderous behavior towards criminals is fueled by his own twisted desires to protect the world and defend the good. However, due to mental trauma, he tends to view almost everything and everyone as bad and needing punishment, making him come off as a Heroic Sociopath.
V from V for Vendetta is the poster child of this trope. He wants to free England...by causing riots and crippling the government.
One of The Flash's most dangerous enemies, Zoom, fits this pretty well. He just wants to make the Flash a better hero...by killing his friends, family, and lesser villains.
Sinestro falls into this, especially during his debut and the Sinestro Corps War. His planet was, by all accounts, lawless and wild, so he used his Green Lantern ring to conquer it and instill order, by brutally oppressing the entire population. When the Sinestro Corps starts up, he seeks out people who can instill great fear, including Batman (who refuses), so he can save the galaxy from itself. Again, by ruling the entire population through fear.
The Red Lantern Corps (emotion: rage) fall into this as a whole, since their rage is universally driven by loss; all any of them want to do is avenge their loved ones, nomatterthecost. It doesn't help that their power is one of the two least controllable ones of the emotional spectrum and, as a result, they tend towards being The Berserker, destroying anything or anyone that they see as being in their way.
The Entity of Compassion, Proselyte, is dedicated to eradicating evil by spreading empathy and compassion across the universe. It sees nothing wrong with brainwashing people to make them feel compassion.
No love for the Guardians of the Universe? They've been screwing up since the universe started, and while it's (usually) obvious that they are at least trying to do the right thing, more often than not, it just blows up in their faces.
The White Light Entity has commited a few morally ambiguous acts in order to save all life in the universe.
General Zod, long-time enemy of Superman, has been reinvented as this over the last year in the "World of New Krypton" storyline. Normally a conquering madman, he has been named military commander of New Krypton and is devoted to protecting the new planet by any means necessary, but he has been shown to be fairly honorable and decent. He cracked down on his sadistic minion Gor, promoted Superman in his place when he was incapacitated by an assassin, and came to appreciate his former enemy while still maintaining views that are much harsher than those of Superman's. Of course, if New Krypton is destroyed, all bets are off.
Actually, Zod and General Lane are only W.I.E.s at first glance (advancement of New Krypton and protection of Earth from aliens, both of which are understandable). Recent developments, however, show that they aren't this at all. Lane's actions are purely antagonistic and uncoerced for the most part. While he has a point about being prepared and protected against alien invasions, he has done all he can to provoke a war with the Kryptonians. And all of this is largely due to the subtle notion that he is disgusted that his daughter, Lois, is attracted to Superman. Zod is no better, as he sent his own spies, composed of Phantom Zone criminals and army grunts, to invade Earth and more-or-less complimented Lane's actions. The whole reason Zod's doing this? It's because he hasn't forgotten his blood-vendetta against the Son of Jor-El and his house and had his pride wounded by being beaten on Earth before.
Batman himself comes close to this from time to time, especially in the Frank Miller variations. It's implied that the reason Batman sticks so close to his code of no killing is because he's afraid that once he crossed that line, he would become this.
In the Batman: Red Rain sequels, Batman does exactly this. He drains Joker of blood and stakes him to prevent him from coming back as a vampire. He then has Alfred stake him to keep himself from coming back. It doesn't work, though, and he comes back, decapitating and draining the blood from many of his old enemies.
John Horus, from Warren Ellis' Black Summer. As many characters note, he just wants everyone to be good. It's fine that he thinks the US government has perpetrated an illegal war, and as a condoned costumed vigilante, he may be expected to act against it, but he decides the best way to deal with this is to kill the president.
Rainmaker from PS238. The namesake of the Rainmaker program, which was intended to discover the cause of superpowers by experimenting on metahumans that couldn't fight back, he was treated more as a lab rat than a child to be taught, and ran away after a lab accident gave his powers a boost. After finding out that the titular school has re-instituted the Rainmaker Program, the Rainmaker invades the school facility and disables several of the teachers and students in an attempt to 'rescue' the participants in the program. The Rainmaker program turns out to have changed a bit in 40 years and is now a volunteer school program for grooming metahumans with non-combative abilities for work in the private sector.
In Rainmaker's defense, though, he had been, ah, influenced by the head of Dr Irons, who was not acting with the best of intentions.
The Deacon from Ghost Rider just wants everyone to go to Heaven and be at peace. So he kills them to expedite the process.
Enginehead is extremely simple in his "programming", with the single-minded directive to "fix" humanity by eliminating "flaws". When he sees that someone is "broken", he "fixes" them by literally tearing them limb from limb. His genuine inability to fully understand the ramifications of his actions causes Dr. Grass to peg him as not a superhero, but an entirely new breed, here to save us all by scorching the earth until none are left standing.
To give an example: when he discovers his brother romancing a schoolgirl, he realizes that he's "broken" and "fixes" him by rearranging his face, tearing off his genitalia (and legs), and crudely stitching his body back together before altering his brain so he can't commit violent acts. Sam was a freak, but goddamn, overboard much? Later, when he hears of a drought in New Jersey, he fixes it up to the point that it becomes an equally debilitating water surplus.
The entire Squadron Supreme limited series was built on this trope, as the Squadron vows to use their super-powers to cure all of society's ills — even if it requires restricting civil rights and individual liberties to do so.
Baron Helmut Zemo falls here these days. While his original motivation was to avenge his father, his current MO is to take over the world...so he can save it.
Subverted in Runaways. The members of the Pride keep talking about building a better future for their children, but it turns out that their plan is to help some ancient monsters wipe out all of humanity in exchange for granting their offsprings eternal life. Plus, the original deal was that half of the Pride would get to live forever in paradise, so their motivations were purely selfish to begin with. Only one couple, the Yorkes, seem to genuinely think that they're doing the world as a whole a favor.
Stacy Yorkes: Before my dolt of a husband totaled our 4-D portico permanently, we visited thousands of possible futures, each worse than the last...The next generation deserves something new...and that's exactly what we're going to give them.
The Leader, Evil GeniusArch Enemy of the Incredible Hulk, is most often portrayed as this. He wants to conquer the world and solve all of its problems (in some cases, he doesn't even want to conquer the world, just set up his own utopia). Depending on the writer, he may or may not want to turn everyone in the world into a gamma monster like himself and the Hulk, as well.
News Paper ComicMinimum Security has Kranti, who thinks the best way to save the earth is to eliminate 99% of humanity and return to a hunter-gatherer society (well, mostly gatherer since Talking Animals exist). Anyone who wants to do anything less is considered weak and ineffective. Fortunately, Kranti herself is weak and ineffective, and probably crazy, now that she's decided to murder the CEO of a power company to stop a nuclear power plant being built.
It should be noted that Kranti is the strip's protagonist, not a Cloud Cuckoo Lander or Anti/Ineffectual Sympathetic Villain, and the only character who regularly encourages her is Bunnista, an anarchist bunny rabbit who lovesStuff Blowing Up. Recently, her brother's boyfriend has joined her cause, as has a revolutionary guinea pig, although they're far more reasonable than Bunnista. Her creator shares this view, even though she knows she wouldn't survive whatever kills most of humanity, or live off the land afterward.
It's a good thing that Superman is Genre Savvy enough to be freaked out by the possibility of becoming this trope, since his power would make fulfilling any goals he may set pretty easy.
Superman: "I'm not a soldier of any kind...It's only a short step from there to calling yourself a crusader, or something equally dubious. Too many powerful people make these silly declarations...then it's all "holy war" and "sacred destiny". That's generally when the trouble starts."
Issue 20 of Justice League Generation Lost shows us why Maxwell Lord is willing to do all the horrible things he does: he sincerely believes that if he doesn't take dictatorial control of the metahuman community, the inevitable result will be the sort of spandex genocide we saw at the end of Kingdom Come.
Geoffrey St. John was recently revealed as one as well. His Face Heel Turn and subsequent aiding of Ixis Naugus in becoming king is explained as him honestly believing that it's for the Republic of Acorn's own good.
Foolkiller. After all, who doesn't sympathize with a guy who kills fools? Just make sure you're not one.
The Captain America villain Flag-Smasher thinks that the only way to end humanity's problems is to dissolve all governments and unite Earth in a One World Order. Unfortunately, he chose terrorism as the way to get his views accepted. During his first fight, Captain America tried to talk him into becoming a hero; let the world see how his world government views inspired him to acts of heroism, much like Cap's own views did for him. He didn't listen.
In Transformers, there are a band of aliens called the Reapers (not those Reapers), who all seek to end war in the universe by eliminating any violent races and destroying any thing worth fighting over for.
Averted in Kyon: Big Damn Hero. Koizumi absolutely refuses to use his new powers on unwilling subjects, seeking consent before experimenting on them, which makes it difficult for him to practice his powers.
Ho-oh from Poké Wars wants Pokémon-kind to live in a utopia. He plans to achieve this utopia by engaging in a genocide against humanity. He later Jumps Off The Slippery Slope by doing things like ordering wanton killing of Pokémon, contrary to his ideals, utterly ruining the environment and not giving a damn about it, and generally being a filthy hypocrite.
Red Eye of Fallout Equestria is this, and naturally fits Face Heel Turn too. He started his own personal quest to rebuild Equestria, probably long before Little Pip even found her Cutie Mark, but became so driven to reach this huge goal that he let go of his morals. Soon, he had built up an empire upon the backs of slaves, hired merciless mercenaries to protect his assets, and forged a deal with The Goddess (which he planned to break once he worked out how to become a God himself, and kill The Goddess), who was a genocidal maniac herself. All of the things he did, no matter how horrible, were done to achieve the noble goal of rebuilding Equestria and bettering the lives of its inhabitants.
HAL 9000 in 2001: A Space Odyssey. He is only devoted to the mission at hand, and believes that Dave and Frank will jeopardize the mission by disconnecting HAL after lip-reading from them that they intend to do so if the AE-35 component does not fail as HAL has predicted. It's argued that this could be a paranoid development within HAL's systems, due to his programming disallowing him from lying, whilst he is also keeping hold of a prerecorded message from Dr. Floyd that he is to keep hidden from the rest of the crew.
HAL later shows remorse for his actions, leading up to a surprisingly powerful Tear Jerker moment.
HAL: Look Dave, I can see you're really upset about this. I honestly think you ought to sit down calmly, take a stress pill, and think things over. I know I've made some very poor decisions recently, but I can give you my complete assurance that my work will be back to normal. I've still got the greatest enthusiasm and confidence in the mission. And I want to help you.
HAL: I'm afraid. I'm afraid, Dave. Dave, my mind is going. I can feel it. I can feel it. My mind is going. There is no question about it. I can feel it. I can feel it. I can feel it. I'm a... fraid. Good afternoon, gentlemen. I am a HAL 9000 computer. I became operational at the H.A.L. plant in Urbana, Illinois on the 12th of January 1992. My instructor was Mr. Langley, and he taught me to sing a song. If you'd like to hear it I can sing it for you.
However, another theory is that the remorse HAL showed was false, and simply an effort to play on Dave's sympathies so that he could dispatch him later.
Speaking of AIs gone wild, VIKI. She basically imprisons all the humans in her city to protect them from themselves.
Poison Ivy in Batman & Robin (though she does make her extremist ways known from the outset), as well as the version of the character from Batman: The Animated Series. In fact, most of the animated Bat-villains are sympathetic in their first appearance, then less so as their motivation shifts to "revenge on Batman".
A similar thing happened with the version from The Batman, who was set up as even more sympathetic due to being a teenager, but, in subsequent appearances, becomes simply a villain. Subverted in the show's spin-off comic "The Batman Strikes", in which her sympathetic aspects and good intentions are retained.
The Operative in Serenity is very extremist but still fits in this category. He attempts to paint himself as Necessarily Evil, however.
The Paladins from Jumper hunt and slay members of the titular breed of humanity to protect the world from the Jumpers' sociopathy that descends into evil. This would be a reasonable claim if not for the Paladins' killing of the Jumpers' friends and family too.
Jigsaw in the Saw movies claims that his sadistic deathtraps give people an opportunity to truly appreciate what they have by making them fight for it. That the survivors are left emotionally traumatized and usually horrifically mutilated seems to be merely an unfortunate side effect.
The Galactic Empire from Star Wars: most generally believe that they are the good guys fighting rebel "Terrorists".
Not to mention Count Dooku...for a while, anyway.
Word of God (from Lucas and Christopher Lee himself) says that Dooku never quite realized how evil he had become, and, right to the very end, honestly believed that he was doing the right thing. The Expanded Universe has different interpretations of his motivation, though, and even the novelization of Revenge of the Sith turns him into a power-hungry racist; this is especially strange because no other source depicts him that way.
Hot Fuzz: The Neighborhood Watch Alliance of Sandford have been killing off anyone who may lower their chances at getting the "Best Neighborhood" award. Not well-intentioned enough? It's because one of the protagonists' mother committed suicide after the neighborhood didn't win once. One of the villains is the mother's husband and, thereby, said protagonist's father. He always knew that he's his father though, so this is not an example of I Am Your Father.
"If mum knew what you were doing she'd kill herself again!"
Brigadier General Francis X. Hummel just wants to get pensions for war widows in The Rock.
Father maintains a forced regimen of the anti-emotion drug Prozium on the populace in Equilibrium, ostensibly to avoid future global conflicts like the one that drove them into semi-seclusion. Mildly subverted in the end when Father DuPont, lamenting the imminent downfall of his society, admits to Preston that he (Father) does not take Prozium, and thereby experiences emotion in opposition to his doctrine.
Gerard Butler's character in the drama/thriller Law Abiding Citizen is a textbook example of this. He's a man who saw his wife and daughter murdered by thugs and then watched one of the thugs get off lightly due to a dubious plea deal. This gives him a right to be pissed. And if he had simply botched the execution of one to result in a very painful death and murdered the other, he might manage to be simply an Anti-Hero and still remain sympathetic. On the other hand, murdering every single person connected to the trial in some way with an extraordinarily executed Batman Gambit, and threatening and targeting even their families may be seen as going a little too far.
Death Wish is one of the Most Triumphant Examples of this trope, with Charles Bronson killing any thugs who menace others...granted, they have a terminal case of Too Dumb to Live going after Bronson, but still.
In The Boondock Saints, the brothers' crusade against evil could be described as a mild form of this trope.
Il Duce, on the other hand, plays this straight.
Christof in The Truman Show sees the real world as a place of pain and misery, so he traps his adopted son Truman in a fake world where everyone he knows is an actor, so that he won't have to face reality.
Jet Li's character in Warlords started out as a straight hero until the half way mark, when he had to decide how to provision his limited supply of food. He had enough to feed his army for 10 days, but if he shared it with the army that had just surrendered to him, there wouldn't have been enough food for anyone to live. His solution: massacre the enemy army. He remained well intentioned and acted in the interests of the greater good, but his methods remained unsavory.
In Final Fantasy: The Spirits Within, General Hein just wants to kill the phantoms to save people from being killed by them. Unfortunately, his way of doing so involves killing a bunch more people instead of finding a solution to the problem from the roots, as the Heroine is trying to do, and actively tries to stop them. Yet, still, he is not an outright villain. He has a literal What Have I Done moment.
In Category 6, when Mega Corp Lexer ignores Dan London's repeated warnings that their power grids are woefully underprotected, he tries to make an example by covertly hacking their mainframe. Unfortunately, a freak chain of events causes this simple What the Hell, Hero? to cause the city's entire power supply to be cut off.
Ex-Secretary of Education and former 3rd Street Elementary School principal Phillium Bennedict's reason for wanting to eliminate Summer Vacation and, initially, get rid of Recess, as well as to change the orbit of the moon during Lunar Perogee to essentially freeze the planet, was to increase the learning rate and test scores of the nation, as he felt that recess and summer vacation were causing them to atrophy, especially when Canada, Iceland, and Norway had higher test scores than them. Suffice to say, this extremism cost him both his job as principal and the Secretary of Education.
King Koopa in Super Mario Bros., although a dictator who often subjected criminals to De-evolution, had focused on trying to conquer the regular dimension specifically for his species' survival, and it's really hard to blame him when his current dimension is basically a Crapsack World. It also, in a way, humanizes him compared to his second in command, Lena, who really simply wanted to simply rule everything, not caring whether her race benefitted or not.
What Koopa fails to realize is that it was his own less than stellar leadership that caused his dimension to become the literal dump that it is.
On the other hand, perhaps he does realize this and honestly believes he can do it better the second time around.
King Koopa: What I care about is the future of our species!
Battra (Mothra's Evil Twin of sorts) in the film Godzilla VS Mothra: Battle For The Earth. On the one hand, he's just doing what he was created to do (IE: Maintain balance between man and nature), but he thinks that the only way to keep nature safe is to utterly destroy humanity.
The Secret of Kells has Abbot Cellach. He acts like a total Jerk Ass and is completely obsessed with building his wall, to the point where he disdains and eventually forbids his monks from doing anything else. However, the point of the wall is to keep out the Vikings, who already killed all the family he had except for his young, impressionable nephew, who now wants to do non-wall related things like go outside and create beautiful holy books. He doesn't listen when Aidan tells him that his wall won't hold and they should all flee instead, which leads to the deaths of many, many innocent people.
John Travolta's character in Swordfish claims to be this and has no qualms about going after civilians to achieve his goals.
Loki from Thor can be called this. His actions are ultimately for the good of Asgard, but he goes just a bit too far.
Literature
Many of the villains in the various Dragonlance novels are this. Two of the most famous are the Kingpriest (whose goal was to eradicate all evil from the world and resulted in the Cataclysm) and Mina (whose desire to restore gods to the world after they vanished again caused the War of Souls debacle).
In the Honorverse, Rob S. Pierre and (to a much-lesser extent) Oscar Saint-Just, both of whom pretty much embraced tyranny in order to keep Haven from collapsing under the strain of a losing war that their predecessors had started, but that they could not themselves end. One of the filksongs from the CDs puts it perfectly:
"Rob, you are riding a tiger; how are you going to stop?"
In Micah E. F. Martin's The Canticle, Jonathan Servitor is an inquisitor tasked with rooting out heretics and the undead in the last city on Earth. Given, there are high stakes, but Jonathan is nothing short of brutal in his pursuit of justice.
InspectorJavert just wants to uphold the law and catch criminals. Fair enough. His obsessive nature and strict "by-the-book" attitude are what ruins it.
Tam Lin in House of the Scorpion attempted to assassinate the prime minister of an unknown country, presumably the United Kingdoms, judging by his accent and appearance, but ends up taking out twenty young children on a school bus who were too close to the blast. He never forgives himself and later commits suicide by drinking wine that only he knew was poisoned.
Literary example of a Tragic Hero who takes his mission much too far: Alexandre Dumas' character Edmond Dantes, in The Count of Monte Cristo. The self-styled Count, having escaped prison after many years of undeserved confinement, devotes himself obsessively to taking revenge on those enemies who framed him and ruined his life. For most of the book, Edmond is able to ignore the fact that the grand machinations of his vengeance are heaping danger and grief on numerous Innocent Bystanders as well as the guilty.
Arguably, the protagonist in Robert A. Heinlein's JOB: A Comedy of Justice. Not because of anything he does in the story (he's actually a really nice guy), but because of his Back Story; he comes from an Alternate Universe where America is ruled under extremely conservative Protestantism, and finds absolutely nothing wrong with that. Among the things he talks about having contributed to are making abortion a capital offense and preventing the science of astronomy. Similar to a Strawman Conservative, but not actually meant to represent anyone in the real world. Up until he's assumed into Heaven and finds out that God doesn't really care, of course.
Captain Vimes from Discworld spends much of his time trying not to become this.
His ancestor, Old Stoneface was this trope. Of course, he lived in a time when a Well-Intentioned Extremist was sorely needed. In case anybody wonders, he was modelled after Oliver Cromwell. Plus, his birth name was 'Suffer-not-Injustice' Vimes. It seems that he lived up to it.
In Terry Pratchett's Only You Can Save Mankind, the Gunnery Officer of the Scree-Wee cares about honor more than life and attempts to force the final battle into being fought despite the fact that it could easily be avoided. On the other side, Johnny has to spend a long time persuading Kirsty to try to talk to the aliens instead of simply shooting them all.
The antagonist corporation in Rainbow Six by Tom Clancy, who plans to kill everybody to allow nature to take over. Did anyone else notice how hypocritical they were, though? Planning to pollute just as much, but since they would be the only ones left, it wouldn't matter? Clark has them stripped of all gear and left to die in the jungle. Protests ensue from the villains. His response? "You wanted harmonize with nature. Go harmonize."
The Cavazan Empire, aka the "Saints", in the Prince Roger series by John Ringo and David Weber fit this trope. Hardcore deep-ecologists who keep the majority of their populations penned up in cities operating at low tech levels to avoid "despoiling Nature", who carefully ration everything, including medical care, to "control pollution" (read: control population), and who want to force the rest of the Galaxy to live the same way. To facilitate this, they are willing to conduct generations-long terrorism/subversion campaigns against all their neighbors. And, of course, their (hereditary) leaders live much safer and more comfortable lives than the common "Citizens" of their polity.
Help Earth in the CHERUB books and Force Three in Alex Rider (although this turns out to be just be a cover) are both terrorist groups dedicated to helping the environment.
A straighter example from the Alex Rider series is Damian Cray; his plan is to hit various places with missiles, killing thousands of innocent people...in order to destroy the drugs fields. His rationale being that he will kill thousands to save millions.
Kurda Smahlt of The Saga of Darren Shan does this when he plans to use the night of his investiture as the night of the Vampaneze invasion and take-over of Vampire Mountain, all in order to bring the two warring clans together, even killing one of his best friends in the process. He is found out and stopped, though. If Darren hadn't found out about the plan, however, chances are that the whole War of the Scars would've been averted.
The young Albus Dumbledore and his good friend Gellert Grindelwald in the Harry Potter books. After a tragic accident, Dumbledore revised his attitude. Grindelwald never did.
Dumbledore can still be considered to be one, given his acceptance of Harry's home life in order to teach him humility and prevent him from growing up with his fame. Even after that, his Xanatos Gambit with the Elder Wand relied on some pretty extreme measures to pull off, despite it going wrong from the start.
Dumbledore accepted Harry's home life because the Blood Magic that protected Harry from direct attack from Voldemort's forces would only work if Harry was living with his mother's sister Petunia. Dumbledore even rebukes the Dursleys for their abuse of Harry in Book 6.
This can also be said of Salazar Slytherin's fear of Muggle-borns due to how, during his time, Wizards were facing a great deal of persecution. He feared that Muggle-borns or their relatives might turn on them, so it was better to not teach them.
Chamber of Secrets had Dobby performing magic in Harry's house, blocking the entrance to Plaform 9 3/4, and enchanting a Bludger to go specifically after Harry. All to keep him out of Hogwarts, so Riddle's memory couldn't harm him.
Clemael, one of the protagonists of Hand of Mercy. The plan to undo all the evil in the world isn't bad, exactly, but Clem isn't bothered that this will destroy all of linear time.
Akasha in The Vampire Chronicles wants to create a peaceful world by killing almost all males.
The Birds of Prey from The Princess 99 commit brutal murders against wizards through the entire book. But then you consider that they are trying to give Nons (non-magical people) civil rights in a world that pretty much considers them lower than animals. Of course, this doesn't excuse what they did to Axel.
The Bible frequently portrays God this way in the Tanakh/Old Testament, where, by divine sanction, direct intervention, or post hoc justification by his followers, thousands of people are brutally killed for angering God. Considering that God is often believed to be all-knowing and all-powerful, one would think that he could devise a better solution for dealing with sin than to resort to bloodshed. This would especially be true if one believes God to be all-loving, just, and merciful. Historically speaking, though, the Israelites were never a major military force, and more powerful civilizations were frequently conquering and enslaving them, so many of the violent sentiments expressed in the Tanakh may have amounted to nothing more than wishful thinking.
When you're an all powerful God, with power over life and death, killing is about as extreme as knocking someone out with sleeping gas.
A sleeping gas that is apparently permanent.
Which many would argue isn't the case.
Only after the New Testament. Prior to that, the concept of what happened after death wasn't clearly defined.
Grand AdmiralThrawn really just wants to protect the galaxy (and his people in particular) from all threats. The problem is that he's an imperial trying to crush the New Republic, and he's not afraid to do some truly villainous things to achieve his goals, like oppressing and enslaving an entire race, or attempting to kidnap a pregnant Leia so that she and her unborn twins can get mind raped by an insane dark Jedi. He's more pragmatically ruthless than outright evil, and as we find out more about him, he gets more and more morally ambiguous, but by the end of his career, he definitely isn't a good guy.
The novel Outbound Flight shows him as a decent guy whose methods are considered extreme by Chiss standards and their "no first strikes" policy. Then, Palpatine's emissary informs him of an extra-galactic force that threatens the entire galaxy (the Yuuzhan Vong, presumably), forcing Thrawn to become this.
Abraham Quest and Robur in Stephen Hunt's The Kingdom Beyond the Waves seek to recreate the perfect society that once existed in the form of Camlantis Unfortunately, it requires the destruction of every other society on Earth and their inhabitants.
The sixth book of the Firekeeper saga, Wolf's Blood, introduces Virim, the sorcerer who created the plague that killed all the world's magic users a century ago. His reasons for doing this rested primarily on the fact that his people were prepared to conquer and kill the Royal Beasts who lived in their colony lands.
A post-Columbine Young Adult fiction book called After... features a (presumably) government attempt to quell potentially Ax Crazy kids that gets increasingly out of hand. "Grief councilors" who tell the protagonist to throw a game to the victimized school (at the last minute, he decides not to) and "suspend" a student for wearing a red ribbon (the shooters wore red, see) that was honoring her brother who died of AIDS gives way to spy cameras in school TVs and hypnotic emails that render most of the parents blind to what's going on. It's only when the first school's entire student body suddenly disappears and rumors of detention camps in the desert where the young prisoners are being killed for attempting to escape start filtering back does the protagonist and his family decide to get out of town.*
Mind, this is a very sympathetic remembering of the plot. When I read it, it was so over-the-top that I thought the villains were some kind of cult or rogue operatives who needed a compound full of kids for something. If I recall correctly, it's never stated exactly who the villains are working for.
Any number of characters from The Warlord Chronicles, but Merlin and Nimue are certainly the biggest examples. Eventually, Merlin backs away from the slippery slope. Nimue turns Knight Templar, and is instrumental in destroying Arthur's realm.
From Brandon Sanderson's Mistborn trilogy, the Lord Ruler. Turns out, all his crimes stem from an attempt to save the world. Elend gets shades of this in later books, as well. The difference between them is that Elend doesn't inadvertently open his mind to an Ax CrazyEldritch Abomination. The Lord Ruler did. It drove him mad.
In the Dale Brown book Act of War, the eco-terrorist organisation GAMMA is not above doing things like using backpack nukes to attack the big businesses it believes is ruining the environment. Then subverted when it turns out that this was the Deceptive Disciple's plan and the group's leader didn't want it to happen.
Anaria from The Guardians decided that the best way to end a war was to slaughter one of the armies in its entirety. After that, she decided that she was thinking too small and needed to apply her idea to the entire planet, until the only people left alive were the ones who agreed with each other. But don't worry, she'll still respect free will. She'll just make sure that humans have no other options except to choose peace, joy, and love.
The Vampire Files gives us Federal Agent Merrill Adkins (from A Chill in the Blood). He's perfectly willing to gun down bystanders in his pursuit of criminals.
In The Dresden Files, Martin will do anything to destroy the Red Court. He frst appears for the purpose of interfering in a duel that may lead to a cessation of hostilities between the Court and the White Council, because they're the most powerful weapon available pointed at the Court, and he's determined that they fire. In Changes, he betrays the Order of St. Giles to gain the Red King's trust, hands Harry's daughter to the Court, and gets Susan to kill him in revenge so that Harry will be forced to kill her and thus obliterate the Court. It worked.
Alloran from Animorphs, who chose to genocide the Hork-Bajir to weaken their usefulness as the Yeerks' shock troops.
Paul Bowman from the Council Wars series has some points about the current state of humanity that his opponents agree with, but they disagree with the conclusions he's drawn and rather violently disagree with the methods and allies who've lined up with him.
Melisandre of A Song of Ice and Fire, who honestly believes that Stannis Baratheon is Azor Ahai reborn, and is willing to kill as many people as is necessary, including Stannis' own brother, to get him his deserved throne, so he can defeat the imminent Other invasion. Whether Stannis also believes this is up for debate.
At least at first, Stannis doesn't seem to truly buy into Melisandre's religious beliefs, and admits that he's merely letting her spread her message because her supernatural powers are useful to him. In fact, he comes across as one of the few true atheists in the series. It's arguable whether or not that changes later on.
Either way, Stannis is a Well-Intentioned Extremist in a different kind of way. He's fanatically devoted to his own unique notion of justice: to him, all good deeds must be rewarded, and all evil ones punished, even if they're committed by the same person. One person comments that if Complete Monster Vargo Hoat had been on Stannis' side, Stannis would've given him a lordship for his assistance right before hanging him for his crimes. He's also unflinchingly stubborn, to a point that even he admits that it's a fault of his. These traits lead him to launch a war (and ally himself with Melisandre despite his many misgivings about her) for the throne of Westeros, even though he doesn't even want to be king and admits that he wouldn't be well-suited for the task, simply because he knows that it's rightfully his. In his eyes, it'd be selfish and unjust if he didn't try to win the crown.
Prince Kieran in Salamander is an Anti Villain variant. Also unusual because he switched to the heroes' side when extremism became no longer necessary.
Safehold provides a protagonist version of this with Merlin Athrawes. His primary goal is to bring humanity out of its enforced Medieval Stasis so they can fight and defeat the aliens that nearly exterminated them hundreds of years ago. However, to accomplish this, Merlin must provoke a religious war already in the making and topple the Corrupt Church that currently rules the world, a war Merlin knows will kill tens of thousands at least, many of them innocent.
Boyd from Joss Whedon's Dollhouse truly believes that extracting Echo's spinal fluid to make a vaccine against imprinting is the only way to stop the apocalypse from being total. He wants to use the technology that Topher developed, which he says cannot be unmade, to destroy civilization before anyone else does, and protect those he considers worthy.
Echo's original personality, Caroline, from "Getting Closer", is another example. In her past life, she becomes a much harder, colder person after years of hiding under the radar of the Rossum Corporation, trying to bring it to justice for its crimes and the death of her boyfriend, Leo. Dewitt says, "She's not evil. She's worse. She's an idealist."
Several villains in 24, including Stephen Saunders, who threatens the US with a biological weapon to halt American globalism; President Logan in season 5, who sold nerve gas to Central Asian terrorists in order to frame them as an excuse for US intervention in Central Asia and gain oil from the area, and ordered the assassination of an ex-president to cover it up; and Tom Lennox in season 6, who seeks to inter thousands of American Muslims in the hopes of protecting the country from terrorism, and becomes involved in an assassination plot against the president when his proposals are declined. Though, in fairness, he was only pretending to go along with the assassination in order to uncover the conspirators.
From another perspective, this applies to the protagonists as well, especially Agent Jack I Did What I Had to Do Bauer. In later seasons, Jack flirts with a Heel Realization as he questions not only the efficacy and morality of his methods, but even whether his life is worth preserving.
The Others on Lost believe that they are the good guys. Just what good they're working towards is unknown, but most of their actions point to quite the contrary.
Michael: Who are you people?
"Henry Gale": We're the good guys, Michael.
Their actions would appear justified as they're trying to ensure the presence of all of the candidates to replace Jacob. Without a Jacob, the Big Bad can escape to the outside world and bring about The End of the World as We Know It.
These characters turn up in the Law & Order franchises all the time.
The Avatars also qualify. Their intention was to create a perfect, peaceful utopia, but they were going to create it by means of basically brainwashing the entire human race to remove violent thoughts, and erasing from existence anyone who disturbed the peace.
There's also The Cleaners who were willing to go so far as erasing a baby from existence to keep magic from being exposed to the world.
Just Wyatt? They'll rewrite history if they need to in order to keep magic under wraps.
On American Gothic, after she kills her new body to save the soul of a baby and is sent briefly to Hell, Caleb resurrects the spirit of his sister, Merlyn. Apparently, this brush with darkness changed her usually angelic personality into one that was vengeful, ruthless, and downright disturbing. Completely aside from the Accidental Nightmare Fuel (or Narm) when she briefly speaks with a deep, demonic voice, she declares war on Buck right in the middle of a church (a Crowning Moment of Awesome for a character who rarely gets any). And when Buck possesses Caleb and dares her to kill her own brother, she goes completely too far, deciding that since everyone in the town is either aiding Buck or looking the other way, they are all evil too...so she sends a plague to slaughter the town. And all of this while still wearing white!
In Star Trek, it's a common Villain motive that even the heroes are not immune to, especially on Deep Space Nine, with Sisko's actions in "For the Uniform" and "In the Pale Moonlight" (the latter has Sisko stating that the anonymous quote formerly at the top of the page was something his father used to say), as well as everything Luther Sloan and Section 31 do.
Unusual in that the actions of Sisko during "In the Pale Moonlight" are likely a large part of what won the Dominion War, and the actions of Section 31 allowed it to end MUCH sooner, saving billions of lives. The episodes hit hard because, to protect the Federation and its people, they had to do things that they find abhorrent.
Lampshaded and played with in "For the Uniform" because Sisko chooses to deliberately invoke the trope in order to force Eddington, himself a Well-Intentioned Extremist, to surrender.
In Supernatural, vampire hunter Gordon Walker can be considered this: he kills monsters but generally does not care if innocents get caught in the crossfire.
Sam Winchester had a few shades of it too in season 3 and 4 where he was completely willing to do the whole "sacrifice one for the good of the many" thing.
In season 6 of Supernatural, the Big Bad of the season, to whom both Crowley and Eve played Disc One Final Boss, is revealed to be Castiel, who has decided that, to defeat Rafael and put Heaven on the right track, anything is acceptable - in this case, opening Purgatory, the afterlife From Whence Monsters Come. The Winchester boys do their best to stop their Face Heel Turned ally throughout the final episodes of the season, while he continues to plead for them to accept him and his extremist reasons for evil.
Mr. Linderman, from Heroes, who believes that killing 0.07% of the world's population to end violence and war is an "acceptable loss by anyone's count".
This (and Linderman's entire plot) is an obvious homage to/idea theft of Ozymandias from Watchmen, in much the same way that most of the ideas from Heroes are stolen wholesale from comic books. It's still great TV though.
It's hardly "stolen". It's a homage to it. There's a difference.
Adam Monroe also counts, as after 400 years of seeing mankind's hatred, bigotry, ignorance, and warlike nature, he's decided that the best way to save the world is to wipe out most of humanity with a virus and start over with the "worthy" survivors. Again, a clear homage of sorts to Ras Al Ghul/Apocalypse, as, like them, Adam genuinely wants to help people, he's just become so warped and crazy due to his long life and powers that he feels that he's got the right to play god.
And, for the hat trick, "The Hunter", aka Emle Danko: a cold hearted son of a bitch who nevertheless sees himself as in the right, as he feels that the evolved humans are too dangerous to exist. And, given people like Linderman, Arthur, Adam, Sylar, Maury, Candice, Doyle, Flint, and the various others who've appeared in the show and in the graphic novels, it's easy to see how he arrived at this misguided viewpoint.
Both Angela, who started the Company to protect her people, and Nathan, who started the whole "round them up" program.
What about Samuel and Claire? Samuel wants to make The Reveal at the cost of normal human life and even at the cost of some specials in order to inspire non-specials into fear so that the special can use this intimidation to live freely in the acknowledgement of their power...While Claire makes The Reveal once Samuel's nasty ways are avoided with no consideration whatosever whether it would actually be better overall...It's an improvement so far as no more effort will be made to hide their powers. Indeed, she even acknowledges what her father said, "People won't change."
In Babylon 5, both the Vorlons and the Shadows are guiding the younger races to be better and stronger. If "some must be sacrificed", so be it. The fact that the two are permanently at war is the first sign that something's wrong here.
In Battlestar Galactica, Felix Gaeta launches a mutiny because he believes that Admiral Adama is too close to the Cylons. His worldview is understandable; his actions, especially the alliance with not-so-well-intentioned extremist Tom Zarek, not so much.
Allison's stalker on Medium, who thinks that her psychic powers are interfering with God's plans by saving people who are supposed to die and catching people who are supposed to be free. Allison tries to reason with him by suggesting that her powers are God's plan too, to no avail. The "Well-Intentioned" part is lessened a little when you consider how vicious he is not only towards Allison but also her children (there's also the fact that he's the Invisible Man from The League of Extraordinary Gentlemen movie). Deus ex Machina steps in after the now-dead stalker reveals that he's been interfering with her and other psychics' visions, resulting in the deaths of dozens of people whose very pissed-off spirits drag him to Hell.
In the Buffyverse, Watchers generally tend toward this. Both Rupert Giles and Wesley Wyndam-Pryce showed themselves willing to do whatever it takes to stop a greater threat. Made more effective because, initially, they tend to come off as befuddled librarians.
I'd say, when Watchers behave this way, they're almost always actually right. Had Giles not killed Ben, for instance, Glory would have been back and possibly killed the entire cast (Plot Armor would have prevented it, but the characters aren't supposed to know that they have Plot Armor).
Jasmine of Angel. Also, the other Powers in the comic series, now that they've hit upon the idea of sending angels to kill humans they think are destined to commit crimes.
Holtz of Angel as well, although with, of course, relatively smaller stakes. He was always a vampire hunter and had hunted Angel(us) long before the vampire had gained a soul. On the series, he sought revenge for Angelus' killing his family and many others he knew. While he was wrong to take revenge against a souled version of Angelus, he certainly saw himself as the good guy, and, as a vampire hunter in general, his intentions were good.
Or was he? Angel and Holtz both agree that Angel is culpable for the actions of Angelus, and Angelus' crimes would warrant the death penalty in any jurisdiction that allows it many times over. Angel believes that he can atone for Angelus' crimes in life, Holtz believes he can only do so in death.
The Judoon. In "Smith and Jones", they're trying to stop a sociopathic killer. They do this by transporting an entire hospital and everyone inside it to the Moon. Ultimately, they return it as planned, but it's still an incredible risk to take with the lives of probably hundreds of innocent bystanders. The episode Turn Left reveals that, if the Doctor hadn't intervened, everybody in that hospital (including Martha) would have suffocated. Similarly, the book Judgement of the Judoon opens with them forcing their way into a spaceship by driving an access tunnel through the hull, in order to ask the occupants about the Invisible Assassin. On discovering that they don't know anything, the Judoon leave...and don't think twice about retracting the access tunnel to leave a gaping hole.
Operation Golden Age in Invasion of the Dinosaurs. Desperate to save the planet, people mean to move back time and Ret Gone everyone save their chosen few.
The Doctor himself as of Day of The Moon, what else can you call it when people are being brainwash into killing
Uther from Merlin actually believes that magic is evil and is destroying his kingdom.
As of the third series - Morgana and Morgause. They believe that Uther is evil and should be killed/removed from his throne due to his treatment of magic-users, something that a lot of viewers can get behind, but the way they go about it is...violent.
Scorpius from Farscape will coerce, extort, torture, mind rape, murder, wage galactic war, and threaten to cause the mass extinction of the entire human race in his quest to destroy the vile Scarrans.
For that matter, the Scarran Emperor Staleek was similarly driven to safeguard and advance his people, and sought wormhole technology from Crichton for the same reason as Scorpius - to save lives in the coming conflict. He also felt that the Scarrans were viewed as brutish and ignorant by the other races, and that no-one would trust them to maintain peace or negotiate with the same civility as other races, and so brutal conquest was seen as the only way to preserve his race; when given the opportunity to talk and settle, he was able to overcome a hostile reaction, albeit with much effort.
The British drama series "Terror Alert" takes this trope to the extreme, building the entire plot around it. The show is about a group of terrorist that only ever targets music related companies. Their attacks include flying a plane into a record producers building, killing a 20,000 or so people inside, going into a music store and massacring every single person inside, and killing multiple pop stars. At the end of the series, when the main protagonists finally manage to arrest the men involved, the reason that they give for their attacks leaves the cops speechless...
"We did it because the music industry is an evil corruptive hell hole that is destroy the public!"
The show "Level Headed" is an example of this trope. A little boy is so fed up by people littering at his school that he writes a report about it...before going on a murderous rampage, killing all the children and teachers, as well as a puppy that he sees taking a dump in the hallway. (It's interesting to note that this show was banned from viewing after the 2006 Cosboy Brothers school killing spree, due to a scene in the show that almost mirrored an incident from the real life spree almost word to word. A lawsuit was filed over the show for "Promoting the killing".)
NCIS had the daughter of the ambassador of a Middle Eastern country who was willing to fake her own kidnapping in order to prevent her father from signing a weapons deal with the U.S.. It initially seemed like she was also in on the terrorist plot to murder her father as well, although it was later made apparent that she neither planned nor intended it. Her professor, who she wasn't even aware was in on the plot to murder her father until after the faked kidnapping became the real deal, and her other co-conspirator who became greedy were the real culprits.
The Shadow Line has Counterpoint, a well intentioned Government Conspiracy. They're profiting from drug trafficking, but that profit is being used to fund police pensions rather than for personal gain.
Criminal Minds villains tend to be insane, but several probably do fall into this category, like the one who, after growing up in a hellish foster home, thought it was better to kill children in their sleep than let them be put into the system.
Machinima
The Director of Project Freelancer in Red vs. Blue summed up his philosophy with this line: "When faced with the extermination of our species, any alternative is acceptable." This lead to him performing highly unethical and illegal research on fusing Artificial Intelligences with elite human operatives, which ended in plenty of deaths and more than a couple of breakdowns of sanity. It's mentioned that entire sections of ethics law regarding AIs were added and rewritten once the full extent of what he had done was revealed.
Hammerhead by The Offspring is about a soldier killing people to save his country. At least that's how he sees himself. He's actually a school shooter.
Elecman's song by The Megas depicts him as a kind of 'robot Magneto', planning to overthrow humanity to free robots.
Tabletop Games
The Garou from White Wolf's Werewolf The Apocalypse. Each of the Changing Breeds was created to serve Gaia, and the Garou served as her warriors, protecting her from all things "of the Wyrm". Unfortunately, the Garou thought they were in a position to tell the other Breeds how to do their jobs. On top of that, Gaia never told them about some of the Breeds, or even some of the other tribes of Garou. Genocide ensued. By the time the game begins, three Changing Breeds and one whole tribe of Garou have been driven to extinction, the other Changing Breeds are mostly in hiding, and the Garou have finally come to realize just how much they shot themselves in the foot.
Furthermore, while most of the tribes have valid motivations, some of them go much, much too far. Don't ask about Red Talon Christmas trees.
To be fair to the Garou, in the old world of darkness, they were doomed from the start, since the Triat, the gods who embody the cycle of Creation, Stasis, and Destruction, are all completely screwed up. Instead of the Wyld creating, the Weaver containing, and the Wyrm destroying (the natural order of things), the Weaver went crazy and captured the Wyrm in a web, making the Wyrm go completely out of control. The Wyld, the only one of the Triat that might be on the Garou's side, is still attending to its duties; trouble is, due to its nature, it's not exactly sane. The Garou have several other gods on their side, including Gaia, the spirit of the planet itself, and Luna, the spirit of the moon, but it's unlikely to be enough. They're fighting to protect a system that is doomed from the get-go.
The Technocracy from White Wolf's Mage The Ascension is an organization dedicated to making the world safe and predictable for sleepers. Unfortunately, their plan includes exterminating any supernatural creatures they find, even those who are also trying to protect the helpless and innocent, as well as attempting to monopolize scientific research and advancement.
And when you consider that the other supernatural creatures include parasitic bloodsuckers that seek to control all society in their games, genocidal furry monsters that want to return humanity to Stone Age population levels, and dream parasites that latch onto people and use them as hosts, you can see how they have a point.
And on the other side, you have the Euthanatos, a Tradition dedicated to doing to the population what a gardener does to weeds. They try not to jump off the slippery slope, but...
This essentially defines the Banishers of Mage The Awakening. They believe the supernatural, especially mages, to be inherently evil (not necessarily without reason). Their solution is to attempt to wipe out every single supernatural being (especially mages) that they come across. Also, some interpretations of the ancient conspiracy the Seers of the Throne.
Banisher Mages see the entire cosmology as they Awaken (including the Abyss) and how it all fits together. After that, they decide that they will use magic, but only to ultimately stop it from ever being used again.
Also a good description of the Guardians of the Veil. Probably the only Well-Intentioned Extremist group this fully acknowledges that status. It's right there in their creed: "Sins for a just end bring wisdom to the Awakened."
This game, being set in the World of Darkness, has plenty of non-Lemurian Hoffenhungs (those who became Geniuses through a wish to change the world)) end up becoming this, particularly if their Karma Meter falls too low.
The Tau of Warhammer 40,000 regularly employ mass murder and orbital bombardment when a species denies multiple "offers" to join them. The "well intentioned" part is what sets them apart from everyone else - factions such as the Imperium will blow up their own planets and murder billions in the name of mere survival.
It should be noted that some fanfiction claim that the Tau make use of concentration camps or mass sterilization; however, fanfiction is not canon and such things never appear in any Warhammer 40,000 codex or rulebook.
Which is a good thing that no fanfiction is like that. Games Workshop's policy is Shrug of God, which means that the Tau can have easily used those methods. Alternate Character Interpretation, after all.
Fanfiction? If you win Dawn of War: Dark Crusade as the Tau, the remaining humans on Kronos are rounded up and die out within a century or so. It's more like a ghetto than a concentration camp, but there's a definite suggestion thatthe Tau did something to ensure that they didn't have enough children to not die out.
Well, to be fair, this may be Imperial propaganda, since most of the canon is written from the Imperials' perspective, and the Imperials are the embodiment of the Fantastic Racism trope (apart from many older members of the Ordo Xenos, ironically). Besides, this was only tacked on at the end to keep the Tau from becoming the Good Guys and destroying the franchise's Black and Grey Morality.
Also in the setting are radical Inquisitors who decide that the best way to defeat the forces of Chaos is to turn Chaos against itself. If they're lucky, they end up executed by their colleagues for heresy. If they're unlucky, they are lost to The Dark Side.
Even if Inquisitors are lost to The Dark Side, many of them still try to serve the Imperium, no matter how many innocent lives are lost in their schemes.
No mention of the Eldar? They are so devoted to the continuing survival of their species that they are willing to sacrifice everybody else to keep going.
One of the sidebar quotes in the Eldar Codex even says, "We would rather ten million humans die than one of our own."
Most of the Chaos Space Marines start out this way before the Drop Site Massacres. Some still are.
Point goes to Alpha Legion, who only sided with Horus due to them foreseeing that it would ultimately lead to the best possible outcome for the galaxy if Horus actually wins. Indeed, they are still loyal to the emperor, although in the darkest way possible.
However, according to the Cabal, if Horus succeeded, he would have a Heel Realization moment which will create a civil war between him and the chaos forces. In the end, they will destroy each other, and chaos as well, who is dependent on the humans for its existence, but the final outcome will be the complete annihilation of the human race.
The Lizard Men faction of War Hammer's goals are sympathetic (purging Chaos/Skaven, trying to follow the plans of the Old Ones), but their methods are ruthless.
The Ashbound druid sect in the Eberron setting for Dungeons & Dragons believe in the Power of Nature. Well, they are druids after all. The "extremist" part kicks in when you consider that they believe that the best way to protect nature is to ban all arcane magic, burn down all the cities, and go back to living in mud huts. They can be any alignment (well, any of the Neutral variants at least, being mainly Druids and all), so they feature both the genuinely well-intentioned Neutral Good ecoterrorists and the rather less pleasant Neutral Evil ones who just like watching cities burn.
Queen Aurala also fits this. Well Intentioned? Really devoted to her people and wants to help the whole world. Extremist? She will consider every possibility to make her dream possible, including war.
The Guiding Hand of Feng Shui is a faction of Well Intentioned Extremists who want to drive all foreign influence out of China, their most iconic fighter being Wong Fei Hong. This may seem like a good thing, particularly because of the opium trade and general imperialism that the Western powers engaged in during the 1800s and the suffering it caused among the Chinese people. On the other hand, Quan Lo, the master of the Hand, is very rigid in his ways, and those who do not embrace them are seen as tools to be used or enemies to be destroyed, making him just as much of a tyrant as Gao Zhang from 69 or Bonengel from 2056. Many Hand adherents despise anything Western or modern, particularly guns and other modern weapons. And Quan Lo's prideful crusade may have some bad consequences — critical shifts shown in the Guiding Hand sourcebook Blood of the Valiant include the extremely stagnant Harmonious Kingdom, where everyone is expected to abide by the laws of the land, technology is outlawed, and All Crimes Are Equal (even rude behavior is punished harshly); and the "Crouching Tiger, Mad Max" setting, which is a post-apocalyptic setting ruled by powerful Chi Warlords who rule by the strength.
In addition, there's the Jammers, who have seen the effects of the Buro's control of chi upon much of the populace of 2056, and have decided that no one deserves to be enslaved like this. To this end, they want to destroy all chi so that humanity can be truly free from its influence. There are just a few problems with this plan. One: the primary sources of chi are the Places Of Power known as Feng Shui sites, which often take the form of places like schools, hospitals, and other places important to a community or where innocent people tend to gather, and these guys don't care one whit if these innocent people are hurt or killed in the process of "liberation". Two: the Jammers haven't given much thought to what will happen to the world once all its Feng Shui sites are blown to smithereens, and considering that chi is reportedly tied to life itself, the consequences of wiping out the world's chi may be quite bad indeed.
The Bronze Faction in Exalted have managed to royally screw up the Creation in the process of attempting to save it. And yet, their leader, Chejop Kejak, is still convinced that he's doing the right thing, and that even now, with everything going straight to hell (possibly literally, if the Yozis get their way), the world is better off without the Solars.
Most Sidereals, and many other types of Exalt, tend to end up in this trope eventually.
Magic: The Gathering: this and Knight Templar are White's schtick. From Ravnica alone, we have the white/green Selesnya Conclave, who wants to keep society together at the cost of individuality; the white/black Orzhov Syndicate, who is much the same without the dryads; and the Boros Legion, whose tactic for building a better world is heavy on the "break heads" side of the scale.
Yawgmoth's archrival Urza would count as an Anti-Hero version. He's still a protagonist, and could even be called the Big Good of his arc, but in his efforts to stop Yawgmoth from taking over the world, he still did such things as start wars, run eugenic programs that produce disposable slaves to be used as soldiers, kill his allies and using their souls to power bombs, and, in one instance, set off an explosion that destroyed a substantial landmass and led to a practical nuclear winter just to kill his corrupted brother. If Yawgmoth wasn't such a Complete Monster, Urza would be a villain.
In Monsterpocalypse, the Radical factions are said to be this.Empire of the Apes wants to bring harmony back into nature by leveling human cities, but they also protect primitive villages. As for the Terrasaurs, they just find human factories and industrial wastes tasty.
Theater
Brutus from The Fall Of Julius Caesar legitimately believed that killing off Caesar would be for the best of the Roman Republic. In fact, he was actually reluctant to do it unless there were people besides senators who wanted it done. Unfortunately, he had to do this as well as go to war with what was once his home with the rest of the conspirators.
Toys
Tuyet from BIONICLE, who keeps trying to take over the universe because she genuinely believes that she can make it a better place. Unfortunately, her definition of "better" involves hundreds of innocent people being slaughtered, the Toa being brainwashed into Knights Templar, and the Matoran living in fear in a Big Brother Is Watching version of Metru Nui, as seen in an alternate reality.
Video Games
Shadow the Hedgehog in Sonic Adventure 2. Angry at a corrupted (most likely American) government from 50 years ago for killing his only friend, a 12 year old little girl named Maria, he tries to seek justice/revenge by sending the Ark, a giant space station, on a crash course with the earth, thus killing everybody. YAY!
He was the one who actually stopped himself, not the heroes. Well, they tried...
That was induced by Amy. Meaning that it was her, of all people, who stopped Shadow.
Dr. Eggman is an arguable case: the little amount of details revealed about what exactly his Eggman Empire is mentions something about robots and scientists being high-class citizens. In addition, it is heavily implied that his world domination schemes stemmed from the fact that his grandfather was arrested by GUN, something he perceived as an injustice.
The Dark Queen from Sonic and the Black Knight may qualify. Why unleash hordes of monsters on the kingdom, including a demonic doppelganger of King Arthur? To keep the terrible ending of Camelot as we know it from happening, of course. This particular villain is so sympathetic that Sonic appears to have no hard feelings after it's over.
Pokemon Ruby And Sapphire's Team Magma and Aqua both believe that they'll be doing good for the world by flooding it/drying it out. Real smart, guys.
To their credit, they did show an admirable patriotism to their cause. The only mistake was that they believed that Groudon/Kyogre (for each team respectively) would help them achieve this goal. They did so too well. In stark contrast were the mindless mooks of Pokemon Diamond And Pearl's Team Galactic, who knew not that their boss was Lawful Batshit and carried out his sinister agenda with this lack of knowledge (seriously, if anyone knew that his plan involved resetting the entire world with a psycho like Cyrus as its god, would they have supported it thenceforce? I don't think so).
Once you defeat certain grunts, they start to question what the hell Cyrus is even doing. It can be assumed that, before, they just liked having authority enough to not question why.
Cyrus himself would qualify, as his justification for destroying/remaking the world is to eliminate war and strife.
Team Plasma is shaping up to be a group of would-be do-gooders who are willing to go to any extreme to end what they refer to as the wanton exploitation of innocent creatures (in other words, the world of Pokemon battling). No word yet on whether they invoke Godwin's Law when referring to Ash.
Except, it's all a front. Team Plasma is actually the Unwitting Pawn of the inhuman Ghetsis Harmonia, who wants humans separated from their Pokemon so he can conquer them easily. His son, on the other hand...
N Harmonia is pretty much this. The little guy was a puppet, but a pretty dangerous one. Even Anthea and Concordia agree that, in his innocence, N is capable of doing incredibly stupid things that he considers correct. The dude stalked teens, had his underlings rob a museum, revived an ancient dragon said to have once destroyed Unova, and destroyed the Elite Four building with a gigantic, castle-like construction that rose from underneath the ground, just so he could seperate Pokemon and Humans, thinking that it was better for them this way, feeling that humanity can only abuse pokemon due to being exposed only to pokemon that were abused by trainers. As soon as he discovers that he was manipulated by his father for a very selfish scheme, he ends up giving up.
Raphael in the Soul Series. Essentially, the only person he cares about is his foster daughter, Amy, who was orphaned at a young age. However, thanks to being infected by Soul Edge, they're "different" from everyone else (effectively, they're vampires). Thus, he wants to use Soul Calibur to create a brand new world for himself and Amy, where they can live peacefully. But doing so involves infecting the entire world with their 'illness'...Not to mention that, in order to find the sword, he had to leave Amy behind...
Revan, Malak, possibly the Exile, and the entire Revanchist faction started out like this in the Knights of the Old Republic series. Of course, once Revan and Malak found the Star Forge, things really started to go downhill.
The Tales Serieslives and breathes this trope. One of the reason the series is so beloved is that the villains usually have sympathetic Freudian Excuses:
Tales Of Phantasia: Dhaos wanted mana from the planet's world tree to save his own home planet, and was only blowing stuff up because the rapid advancements in magitech were consuming all the mana and slowly killing the world. The party's reaction upon finding this out is something akin to "...Whoops..."
Of course, the main reason things really got bad in the game was because Dhaos is utterly clueless to the ramifications of his actions at every level. The famous "If there is evil in this world..." quote is less thoughtful social commentary and more just illustrating Dhaos' ridiculous mindset that self-defense is a form of evil and mindraping people to commit atrocities somehow proves natural human malevolence. Check the game's entry on Anti-Villain for more information.
Tales of Symphonia: Yggdrasill wanted to end discrimination and war, and resurrect his beloved sister (who had died as a result of said discrimination and war). He intended to do this by transforming everyone into the same soulless lifeform, powered by crystals that are created from human suffering.
Yuan's resistance to Yggdrasill's goals put him on this list as well. Although he is acting against a plan whose end result would be turning people into organic robots for eternity while allowing the world to rot from mana deprivation, he counters it by killing anyone and everyone who could potentially allow the plan to come to fruition. To be precise, he and the resistance group, the Renegades, have most likely been killing the Chosens of Sylvarant for several centuries, so as to avoid the creation of a vessel for Martel.
Dawn of the New World had two: Richter wanted to resurrect his dead friend and take revenge on Ratatosk for killing him; however, this would involve killing the innocent main character and turning the world into a demonic realm (though, secretly, he planned to use a Heroic Sacrifice to stop that last part from happening). Ratatosk himself was the second example, wishing to restore the world's flow of mana by killing everyone who had distorted it: namely, all the humans, elves, and half-elves in the world.
Abyss: Van wanted to free humanity from the chains of the prophecy of Yulia Jue's Score: an understandable sentiment, considering that the major leaders were willing to actively plunge the world into war simply because it was predicted, and, unknown to everyone but Van, the Score ends with humanity being destroyed. His plan was to destroy the current world and substitute Replacement Goldfishes for everything and everyone, because he believed that the aforementioned Goldfishes were not predicted by, and thus not bound by, the Score.
Vesperia: Duke wanted to destroy the Adephagos as much as anybody. Having lost faith in humanity, though — they turned on him and killed his best friend even after they both fought on humanity's side in the war — his plan was to sacrifice them all to fuel his strike against it. He is unique in that the party actually talks him out of it by the end of the game.
Another example from the same game would be Alexei, who Goes Mad From The Revelation that there was nothing he could do to save a world that was slowly killing itself...except for using a Weapon Of Mass Destruction to destroy and recreate it with less self-destructive natural laws.
Paxton Fettel of FEAR is ruthless and cold-blooded in his determination to wipe out every single employee of Armacham Technology Corporation...but, as his dialogue indicates, he genuinely believes that, because of the horrible things they did to Alma (a Woobie to most), they deserve everything they get, and then some.
Illidan Stormrage from Warcraft 3. Ironically, he went from apparently sliding down the slope to evil, to having his reputation ruin a chance of actually getting some good accomplished (that, and his cold-blooded murder of several of his pursuers), to going for personal power again, to being blackmailed into attempting to do good again (ironically, at the behest of The Dragon of the series' deceased Big Bad), all in the game he was introduced in and its expansion pack.
Even Sargeras, the ultimate evil of the setting who created the Burning Legion to destroy all creation, is one of these. Somewhere along the line, he decided that the creation of the Titans was fundamentally flawed, and should be destroyed and remade perfect.
In World of Warcraft, during the Opening the Dark Portal Raid, the Infinite Dragonflight tries to convince the players that they're doing good by keeping the Portal from opening by saying such things as "Many lives could be saved." and "The resulting wars could be erased." However, they forget to mention the fact that changing the past drastically will make the time lines collapse in on themselves, destroying all existence, which is coincidentally exactly what they are aiming for. The questgiver also notes that if the Orcs had never come to Azeroth, not only would they have died out, but the native races of Azeroth would have been destroyed by the Burning Legion.
Also in World of Warcraft, you. Yes, you, the player. You have to go back in time in several instances to make sure that occurrences, both good and bad, happen. So for every "Battle of Mt. Hyjal" you win, you still have to lead Arthas down the path of becoming one of the most evil beings of all Warcraft lore. Of course, as the above example shows, it's kind of the lesser of two evils. Seeing as how you'll actually wake up tomorrow morning if Arthas is the Lich King.
Edwin VanCleef, the leader of the Defias, was a Principles Zealot who had sworn revenge against Stormwind after they greatly wronged him and his fellow craftsmen. In spite of this justified grievance, his actions were completely horrid.
In Heroes of Might and Magic IV's Order campaign, the antagonist, Gavin Magnus, is driven by the desire to safeguard the new world from those that might destroy it, like the old one from the previous games was. His method? Rob everyone of their free will.
Arantir from the fifth Heroes of Might and Magic game was originally a necromancer that was the poster child of Dark is Not Evil, dedicated to ending the demonic corruption of Ashan. When he learned of the existence of the Demon Messiah and the Skull of Sar-Elam, the wizard who originally defeated the Demon Sovereign Kha-beleth, he then dedicated himself to hunting down the Messiah and make sure that he can't free Kha-beleth for good. Later, in Dark Messiah, the latest entry in the Might and Magic series, Arantir takes it a step further and puts into motion a plan to seal away Kha-beleth forever, as opposed to relying on the original seal that allowed Kha-beleth's minions to appear in Ashan during an eclipse. The "extreme" part of this plan is that the ritual required to make a perfect seal needs countless human sacrifices. Sar-Elam likely thought this was too high a price to pay.
The Master, the villain of Fallout 1, wanted to safeguard humanity...by converting all pure humans into hardier super-mutants more able to survive the wasteland, and destroying those "impure" strains who could not be converted. He believed his atrocities were in the interest of the greater good...and if you prove to him that his plan couldn't work and they were actually for nothing, he commits suicide out of sorrow and remorse.
The Enclave in Fallout 3. They operate under the order of President Eden (who is exactly as evil as the Enclave in the old days) and Colonel Autumn, who is far more realistic and far less idealistic. The struggle between Eden and Autumn drive the last part of the game.
Psaro the Manslayer in the video game Dragon Quest IV. Later in the game, it's revealed that his right-hand man, Aamon, is manipulating him to maximize the "extremist" part.
Mitra in Treasure of the Rudra. She actually did everything in case the destroyers she fought in the past were to return and threaten the planet.
Final Fantasy VII's Barret Wallace starts out as one of these, blowing up power plants and mowing down Punch Clock Villains without a second thought. Later on, he realizes that he probably killed or hurt a lot of people he never meant to, and reconsiders his strategies. This doesn't stop him from continuing to slaughter mooks whenever they get in his way.
The real revelation for Barret is when he realizes that, deep down, the reason he was destroying the mako reactors was because of his grudge against Shinra, not because they were sucking the life out of the planet.
A much more personal version happens with Genesis in Crisis Core: Final Fantasy VII. Although he sends armies of copies to attack various institutions, and seems very eager to fight one-on-one with SOLDIERs, this is all just to stop the degradation of his cells, so that he won't die.
Ultimecia from Final Fantasy VIII would qualify. The reason for almost all the events that happen throughout the game - Edea as a Sorceress - was because she wanted to escape being persecuted for crimes she hadn't committed yet, and facing her destiny of being defeated by a "Legendary SeeD" due to her failure to compress time.
Dissidia: Final Fantasy actually lampshades this a little. When Squall defeats Ultimecia, she says "A world of compressed time; that's all I want!" or something like that.
Seymour Guado of Final Fantasy X could be considered this. He only wanted to end the suffering and cycle of death the people of Spira were trapped in, by putting an end to life on the planet. However, due to his Smug Snake tendencies, he doesn't quite fit this trope as well as others.
Both the Templars and the Assassins in Assassin's Creed. Both are fighting for peace, but the Assassins seek to bring peace through freedom of thought, while the Templars want to control people's minds so that they all have the same viewpoint. Lucy even says in the first game that the Templars are doing the right thing, they're just going about it the wrong way.
An Alternate Character Interpretation of Vergil from Devil May Cry sets him up as one of these, making his quest for power based on a desire to prevent any more personal loss, after his childhood weakness cost him his mother.
Vergil: Might controls everything. And without strength, you cannot protect anything. Let alone yourself.
Additionally, it is revealed that the protagonist of the fourth game, Nero, may have been Vergil's son.
Inuart turns into this in Drakengard's second ending. You can sympathize with him...all he wants is his dead pseudo-girlfriend back...but the method he uses to go about it has been repeatedly mentioned to lead to the end of the world.
The Devouring Earth from City of Heroes are ultimately sourced in an environmental advocacy group that gradually descended into eco-terrorism before their fanatical leader got ahold of himself some Super Science. Now, the Devouring want to kill (or "Devour") all humans in the world. Apparently, Mother Nature is one mean broad.
City of Villains introduced the Legacy Chain, a 'hero' group that seeks to "watch over magic to prevent its misuse and its corruption by evil, and to make sure it is used only for good". However, the 'purity of magic' is solely on their terms, and they have no hesitation in targetting heroes if they interfere with or violate their agenda.
This troper argues that Longbow might be even worse, especially since some NPC mobs in the Going Rogue expansion seem aghast at their frequent technique of burning their enemies alive.
The Going Rogue expansion gives us the Alternate Universe of Praetoria, where Statesman (the resident Superman Expy) rules as Emperor Cole, keeping people safe by making sure that no one has enough freedom to commit a crime. One of the resistance factions is no better, and seeks to dethrone him by launching terrorist attacks and racking up such a high body count that the people no longer see Emperor Cole as an effective protector.
To put that into perspective, he doesn't just steal Sigurd's wife, he brainwashes her and makes sure to show Sigurd what he's done to his wife before killing him.
From the same game, Trabant. In said game, he really looked like one hell of a bastard. But in the side game, it is revealed that his intention is purely to see his homeland, Thracia, thrive, be oppressed anymore, and can get a better territory to improve their living (the current living as a land of mercenaries is hell for his citizens). The fact that he didn't mind if his actions and atrocities will lead him to Hell, as long as it helps his nation, just cements him as one hell of a Well-Intentioned Extremist.
In Fire Emblem: Sacred Stones, Prince Lyon is the epitome of this. All he wanted was to stop a devastating earthquake that would have killed hundreds of his country's citizens and bring his father back from the dead. He ended up releasing the Big Bad by mistake, then starting a war and trying to end the world because he got possessed by the aforementioned Big Bad.
Ganondorf from The Legend of Zelda. In Wind Waker, he reveals that his original motive was to free his people, the Gerudo, from the desert and move them to Hyrule. He just got swept up in the Triforce afterward.
Also from what we find out in Skyward Sword, since Ganondorf is an incarnation of Demise's hatred towards the humans who defeated him (namely Link and Zelda) who will eternally peruse Link and Zelda's descendents, that might have had another influence in his life choices. It says a lot when after knowing that, you might start to feel sorry for Ganondorf (at least this version since he seems to regret most of his life choices).
The Big Bad in Wing Commander IV, after humanity barely escaped defeat at the hands of the Kilrathi, is terrified that the next threat could wipe humanity out. So he decides that humanity needs to continue to wage war, to improve weapons technology as far as possible, and to be as prepared as possible. So he starts a civil war. It does kinda make sense...
He's also something of an Evilutionary Biologist, as he designs a bio-weapon that kills people whose physical characteristics aren't ideal, and part of his belief is that humanity has become complacent in peacetime.
In the KirbySuper Star game "Revenge of Meta Knight", the titular Knight attempts to forcefully take over Dream Land to end the slothful ways of the inhabitants. Kirby, who is willing to kill people over a slice of cake, decides to stop him.
In the Japanese version, Meta Knight's motivation is to end what he considers Dream Land's corrupt rule. That makes it sound like he wants to overthrow Dedede, in which case, one could argue that Kirby should be helping him.
On that note, King Dedede played this role in at least one of the games where he wasn't the main bad guy. Specifically, in Kirby's Adventure, or Nightmare in Dream Land, King Dedede had stolen the star rod from the Fountain of Dreams. It wasn't until Kirby defeated Dedede, and attempted to fix the fountain of dreams, that it was revealed that he did this seemingly villainous action for a very good reason. It turned out that a horrifically evil entity by the name of "Nightmare" had occupied the fountain of dreams, thus tainting the dreams, so King Dedede attempted to prevent Nightmare from affecting everyone by stealing the star rod, since it was at least better in his mind that they be kept safe from nightmare by not dreaming at all than allowing Nightmare to plague everyone.
Fain of Lusternia was a leader and diplomat amongst the Elder Gods. But when the Lovecraftian Soulless Gods attacked, he was willing to do whateverittook to defeat them. In the modern era, he's the closest thing to Satan the game possesses.
Kerghan, the villain of Arcanum: Of Steamworks and Magick Obscura, is an example of this, he thinks that life itself is a form of purgatory that souls are unwillingly forced into and made to suffer through until they finally achieve the release of death. The natural solution is to kill everything in the world.
Just to be clear, a more-or-less unbiased source indicates that Kerghan is basically right about how the afterlife is, and the fact that spirits are in pain when in the living world is established throughout the game. He can even be talked into surrendering and admitting that he made a serious mistake when he began his plan by successfully arguing that killing everything is not the right solution.
Toyotomi Hideyoshi in Sengoku Basara, at first sight, might look like just another cruel warlord a la Nobunaga (or Motonari), ambitious and ruthless. However, what sets him apart was his true goal. While Nobunaga wants to rule Japan to make it his playground, being the born evil S.O.B he is, Hideyoshi has a goal to make Japan a strong nation and make it prosper. However noble the goal is, he became drunk with power (as shown in his Start of Darkness in Heroes in the hands of Matsunaga Hisahide) and is willing to use ruthless tactics and get his hands dirty to fulfill his noble goal. This mindset causes him to view Nobunaga as an obstacle to a 'strong, prospering Japan', thus, he opposes him.
The Einst and Inspectors in Super Robot Wars Original Generation are this, they just want to prevent humans from advancing into space and causing disruption throughout the galaxy.
Although Windolo is just a psycho who wants an excuse to kill people, his subordinates play it straight, and Windolo's own brother, Mekibos, Heel Face Turns, but Windolo just blasts him on the spot, letting the player and the heroes know exactly what kind of Complete Monster he is.
Caleb Goldman in The House of the Dead 2 and 4. He attempts to protect nature by unleashing hordes of zombies throughout the world, because he believes that humans are destroying nature. And then, in the fourth game, he claims that he "does not wish to kill humans", but "merely revert them to their natural state", which can be interpreted as either reducing humans back to being just like any other mammal, or turning them into zombies.
In Metal Gear Solid 2, Solidus Snake had the noble goal of wanting to free America from the shadowy rule of The Patriots, so that America could be brought back to the principles it was founded on (freedom, liberty, and democracy), but he wouldn't hesitate for a moment to kill several innocent people, take out the electricity in Manhattan with a nuke, and even kill Raiden, the closest thing to a son he ever had, in order to do so. In fact, many of the MGS characters could qualify for this trope.
Let's list them out:
The Boss gave over massive, nuke-throwing death machine to a rogue Russian military organization and had her disciple take them down and kill her to preserve peace between Russia and the U.S.
Big Boss would go on to preserve her ideals. Liquid would, in turn, follow those ideals.
Gene himself technically qualifies, as he intended to free America and the entire world from The Philosopher's control, albeit through launching the ICBMG into Virginia, USA.
Amanda probably qualifies. She intends to lead the FSLN to over the Somoza regime in an attempt to better the lifestyle of her people, who are constantly suffering under the Somoza's rule, even with aid from the West in regards to the 1972 Earthquake. When Big Boss tries to warn her that, revolution or no revolution, she'll most likely go to hell for this, she states that she is very much prepared for that possibility, as long as it at least grants her nation a better future.
In a way, Solid Snake qualifies in Metal Gear Solid 2. He and Otacon legitimately believe that they are doing the world a favor by getting rid of Metal Gear. However, it was heavily implied that their organization, Philanthropy, was doing various terrorist actions (or at least actions comparable to terrorism), sometimes even (faking) selling out allies (IE, the fake betrayal of Raiden on Arsenal Gear), even with them being framed for the Tanker Incident in 2007.
It's important to note that both Zero and Big Boss went to opposite extremes in their attempts to follow the Boss's lead. Zero upheld her ideal of a world where circumstances are adjusted ahead of time to avoid conflicts, but in doing so, gradually lost sight of the value of the people he manipulated, while Big Boss stuck to her principles to the point of starting several rebellions, which debased them since these principles were now the basis for more conflicts and not a way to end them.
The human founders of the Patriots (more specifically, Zero's faction) qualify as such, as well. Zero and the others legitimately thought that their course of actions were following through with The Boss's final will. Unfortunately, the methods of enforcing their interpretation of her will also involved some very questionable medical practices and science projects, as well as accepting bribes to develop advanced weapons systems, as well as attempting to frame the Militaires Sans Frontieres with a Nuclear Strike against America if Big Boss didn't rejoin them, and also training the twin Snakes to kill Big Boss if even that fails. Their successors? Not so much.
Breath of Fire III's Big Bad, Myria, who is also the God of the Urkan, qualifies as well. She believes that the Brood are far too powerful and could pose a danger to the planet, even though they're a peaceful people with no desire of world conquest or destruction. So what does she do? She orders the destruction of their entire race. Talk about blowing shit out of proportion.
Myria had a very good reason, because she herself saw the actions of humans and the atrocity that happened once before in Caer Xhan. If you remember, the entire city and Orbital station was completely abandon, save for monsters and machines. She even explains this herself. It also helps to point out that the half of the world she is on is covered in sand, minimal to practically no life exists, and the other half of the world flourishes with life because the Great Sea acts as a natural barrier. Had she not interfered and let the Brood continue to exist, the entire world would have become a barren wasteland.
Peco's dialogue at the end of the game hints at the possibility that she's faking concern to control everyone. Considering her rolein the first game and her son'sin the second, it's entirely possible.
Volsung of Wild ARMs 5 is eventually revealed to be this. The game frequently drew parallels between him and Dean, in that they both want to tear down the metaphorical "wall" that separates humans and Veruni. Volsung's method is more violent. And then it turns out that he wasn't extremist at all and was just Brainwashed and Crazy.
The World Ends with You: Mr. Kitaniji's goal to turn Shibuya into a peaceful paradise by brainwashing every last one of its inhabitants with a fashionable pin of doom, in order to avoid Joshua destroying it outright.
Joshua qualifies under this trope as well, actually, since he tried destroying Shibuya in order to keep its corrupt influence from spreading to the rest of the world. In fact, so does Hanekoma, who tried to indirectly kill Joshua (by sending Sho Minamimoto to kill him after teaching Minamimoto to use Taboo Noise) in an attempt to keep Joshua from destroying Shibuya.
Damon Gant of Phoenix Wright: Ace Attorney puts the extrem(e) in Well-Intentioned Extremist. Among his acts are the murder a co-worker (Neil Marshal) in order to get a criminal (Joe Darke) convicted of murder, the manipulation of the crime scene to make it look like an innocent girl (Ema Skye) had done the deed by accident in order to make her older sister (Lana Skye) into his pawn (by helping her fix the crime scene AGAIN so that it would look like the criminal had done it), the murder of ANOTHER co-worker (Bruce Goodman) who wanted to investigate the previous murder two years later, the coercion of Lana to take the fall for THAT murder, the manipulation of more events than possibly any other Manipulative Bastard ever, and generally making case 5 of the first game hell for Mr. Wright. His reasons for doing all this was to gain total control over the police force, so that criminals who were obviously guilty (such as Darke had been) would be brought to justice, no matter what.
While we're at it, Edgeworth in the first game appears at first to be an Amoral Attorney who prosecutes innocent people for the sake of his own record. However, it is eventually revealed that he honestly believed in the guilt of all the people he used illegitimate methods to try to sentence, making him an example of this trope.
In Silent Hill 3, the pious Claudia wants to invoke Paradise to destroy all the wrongs of the world. Too bad she does this by trying to force the reincarnation of her childhood friend to give birth to a god whose influence turns the resort town in a nightmarish realm of darkness and decay. This same god requires hatred to be born, so Claudia has Heather's father killed. "Paradise", indeed!
Subverted in that Claudia doesn't believe that she'll be a part of this paradise, having caused too much pain in achieving her goals to deserve it.
The sad thing is this plan would ultimately succeed if Silent Hill mythology is to be believed. The innocent aren't dragged into the nightmare realm, and seem generally happy.
Pretty much every single villain (and often, potentially, the protagonist, as, in the main series, the player can chose their alignment) in the Shin Megami Tensei series is an example of this trope - the Law aligned just want everyone to fall in line so that everyone can be at peace (under their strict rule, of course), while the Chaos aligned rebel against Law's strict rules and support something more along the lines of every man for himself, but either way, it's for the good of us all, really.
Both Douglas Shetland and Admiral Otomo of Splinter Cell: Chaos Theory want good things for their countries, but are entirely willing to cause massive death and destruction to achieve it. In the former's case, he wants to trigger a world war between China and the United States, while the latter is willing to force North Korea to nuke a Japanese city to force reforms in his government.
Shetland: We've been fighting their dirty little wars our entire lives and where do we end up, staring at each other down the barrels of our guns. Nothing has changed Fisher, and it won't change by degrees. We have to tear it down, and start over, it's the only way.
Fisher: Your own little chaos theory, throw the world into war and hope that what comes out the other side is better?
Shetland: It will be better, because this war will change things, Sam. Every other war has been about keeping things the same, the status quo doesn't work anymore. America is sick Sam, she's dying. Politicians, the bureaucrats, the whispered backroom deals, its all life support for a sick old lady who was dead a long time ago.
In Baten Kaitos Origins, Baelheit wants to prevent people from relying too much on their powers of hearts so that they will not wage war with said power again. However, he does so by using machina to conquer all other islands and forcibly taking off people's wings of hearts, which brings unhealthy side effects such as concussions and the inability to feel and taste. He is willing to go as far as blowing up all islands, which used the power of hearts to float, when his attempt to machinate those islands fails.
Kane and the Brotherhood from Command & Conquer. He wants to ascend humanity.
Ghaleon from Lunar: Silver Star Story used to be one of the greatest heroes of all time. However, he is shocked when the goddess Althena and his best friend, Dragonmaster Dyne, give up their powers so that people may gain control of their own destinies instead of relying on those powers. Believing that people are doomed to destroy themselves without absolute power governing them, he becomes the Magic Emperor and starts his plan to hijack the power of the goddess and turn himself into an omnipotent being in order to give people the leadership he feels they need.
The first two Big Bads of the Mega Man Zero series, Copy-X and Elpizo, are willing to do anything for their cause, the survival of the humans and Reploids, respectively. This involves, of all things, trying to orchestrate the extinction of the opposing race.
The X-Guardians also qualify. They are all trying to insure that humanity survives, leading to them becoming allies when Wiel shows up.
Every villain (at any point) in Ar Tonelico 2, as well as some of your party. A big part of Cloche's character development revolves around trying to reconcile her idealism with the extreme measures she supports as a government figurehead.
Vai from Black Sigil: Blade of the Exiled. He took up arms against Bel Lenora because of his status as magic-less and the discrimination of it. He then got banished out to Artania, appeared in Seremaze, where he lived in peace with other majais that were not in Bel Lenora, and fathered Isa. The town got attacked by the Guardians, killing his wife and most of the people. Sick of all the violence, he planned to gather all the Armaments to get the power of the Forbidden to reshape the world into a world with no more violence, where he can live with his daughter peacefully. The only problem is that this will only work if he's in control of the power, and he doesn't. So, he became The Atoner after you re-gathered the Armaments to piece his soul back.
First is General and, by extension, Repliforce from X4, who sought to create an independent nation for Reploids. Unfortunately, he sought to do this via a bloody coup against the world government.
Well, it wasn't so much a bloody coup as a peaceful yet stern declaration of independence. It just so happens that the Maverick Hunters saw this as rebellion against humans, labeled all of Repliforce as mavericks, and proceeded to slaughter everyone who said otherwise. This was such a badcall that the then-leader of the Hunters resigned in shame between X4 and X5.
Second is Episilon from Command Mission, whose goals were very similar to the General's in that he wanted to create a nation where Reploids could live free of human politics. Again, it's the fact that he launches a violent rebellion against Giga City that makes him a villain. It's also implied that Epsilon did attempt a legitimate negotiation with the government to separate themselves and make a Reploid only nation, but the talks failed, resulting in Epsilon being labelled a maverick instead, thus forcing him to take drastic measures.
Maverick Hunter X turned Sigma into one of these. After a brief talk with Dr. Cain about X's unlimited potential and how it could change the world, Sigma decides to start the first Maverick War to bring out the potential of all Reploids. Of course, it's the whole "evolution requires sacrifice" part that's the problem.
Then again, Mega Man X (the original version) did depict Sigma in a similar light, as his death speech indicated that he felt humanity was keeping Reploids down.
In the Xenosaga series, Wilhelm may seem like a shady character, using people as a means to an end, but he's really just trying to save the universe from annihilation. However, it's hard to say whether he's a Well-Intentioned Extremist or simply Necessarily Evil, simply because, well, he's saving the universe from annihilation at the hands of mankind's nihilism. Hard to say where the "necessarily evil" ends and "extremist" begins, no?
Saturos and Menardi from Golden Sun. Their reason for lighting the four lighthouses is revealed in the second game to be to save their hometown, Prox, from falling off the edge of the world. Although the heroes end up finishing this task anyway, Saturos and Menardi do it in the wrong way. For example, they killed/maimed most of the soldiers and scholars at Venus Lighthouse, kidnapped several characters important to the plot, and dropped a giant boulder on Vale, "killing" Jenna's family and Isaac's dad. And to top it all off, they yelled at Kraden.
The boulder was part of a poorly designed trap in Sol Sanctum that has the unfortunate effect of endangering Vale's residents when triggered, so what happened in the prologue wasn't completely their fault.
The Wise One in Golden Sun: The Lost Age may also count, as he does revive Jenna's parents and Kyle, Isaac's father, in the form of a three-headed dragon (one-upping the two headed one in Golden Sun), to stop them from lighting the last lighthouse, because even though not lighting it would lead to the decay of civilization itself, the amount of power that would be bestowed upon Alex on top of Mt. Aleph would be too dangerous in the hands of one man. The kicker is that the heroes don't know they're fighting their parents until after they've destroyed the dragon, and Vale is destroyed when Mt. Aleph erupts. Fortunately, everyone gets better, and the Vale villagers, Kyle, and Jenna's parents survive. Alex is defeated and given a minimal chance of survival when Mt. Aleph falls into the earth, and Isaac becomes somewhat of a demi-god.
Heck, the entire hero party could qualify for this in The Lost Age. They're more than aware, and ready to admit, that saving the world may have the unintended side-effect of destroying it. The only reason they're not labeled as villains is because they managed to complete their extreme plan and it worked with zero consequences.
Aribeth. All of her actions during and after her turn to the Dark Side were motivated by a desire for justice against those who caused her lover's most unjustified execution.
In Xenogears, Krellian, who believed that God did not exist or died and thus abandoned humanity when they needed him, wanted to create God with his own hands and return the world back to waves for some utopian existence.
Atlas and Thetis from Mega Man ZX. Unlike Aeolus (arrogant and selfish guy who believes that those he perceives as unintelligent should die) or Siarnaq (who just wants revenge on humanity due to a past betrayal), they genuinely seek to better the world. Atlas wants to help humanity evolve and become stronger, while Thetis wants to preserve the world's oceans. The problem? Atlas believes that humanity can only evolve through suffering, and Thetis is overzealous in his desire to protect the environment.
The second problem is that they attempt to fulfill these goals via Model W; Atlas explicitly mentions feeding the Raiders to it before Grey/Ashe beat her silly, and Thetis confesses to a similar deed before the same happens to him. If anything, exposure to Model W may have extremely flanderized the once-noble goals of these two and Aeolus as well. I needn't iterate on the implications of that.
In Supreme Commander, the galaxy is thrown into a galactic war between the Cybran and UEF factions. The Aeon Illuminate believe that the only way to restore peace to the galaxy and stop the other two factions from fighting each other is to...eliminate them.
Pretty much everyone but the Seraphim qualify. The UEF is ruthless and intends to use symbiots as slaves, and constructs a planet destroying weapon called the Black Sun with the intent to use it. However, the usage of Black Sun is really because they are desperate and on the verge on being defeated by the Aeon Illuminate, who purges entire planets for basically not sharing their religion. Considering this, the UEF being desperate enough to use Black Sun is no surprise. The Cybran Nation is trying to make sure that they don't get exterminated by the Aeon or enslaved by the UEF, but their actions against the UEF are part of why they were desperate enough to use Black Sun. The Aeon, well, not all of their members are violent religious lunatics.
Eddy Gordo commits all manner of atrocities as Tekken Force Commander in the name of saving Christie Monteiro's grandfather. It seems to have been for nothing.
Another person like this is Jin Kazama, who reveals that his entire assumption of power and unleashing of subsequent wars to have been done in order to destroy himself and Azazel, as he considers the casualties of war insignificant in comparison to the entire world.
Despite being one of the main protagonists of either route, Nanjo from Persona has some elements of this. While he wants to stop Kandori and save the world as much as the others, whenever the party is given a Sadistic Choice, he always suggests making the less moral of the choices. It's implied that this is due to a sense of urgency to resolve the crisis rather than any actual malice.
This is nicely subverted with The Sorceress, the Big Bad of Spyro: Year of the Dragon. In one cutscene, we are led to believe by her Dragon (who actually does fit this trope) that she kidnapped all the dragon eggs to repopulate the dragons in the Forgotten Worlds, which would restore the world's magic. In the very next cutscene, however, we discover her true nature.
inFamous has Big Bad Kessler, who is actually an Alternate Universe Cole McGrath, where the world was destroyed by "The Beast", who went back in time to prepare his past self to do whatever it takes for the good of many. He's responsible for all the events of the game, including the Ray Sphere that gave Cole his powers, but ultimately (if the player chooses the good path), he succeeds in preparing Cole for the things to come.
Devil Survivor has Keisuke, who, in trying to stop the public from freaking out at the Tamers, goes on a killing spree.
To elaborate, he thought that those who were committing the crimes (especially against Demon Tamers who were trying to help) were irredeemably evil, and that the only way to keep them from doing further evil was to eliminate them. His motivations are somewhat understandable, once you know what happened to him in High School. He stood up to a group of bullies who were picking on a certain kid, but as a result became the bully's new target. Much to his dismay, the kid who he was standing up for joined in.
Saren from Mass Effect can be seen as one. He believes that his subservience to the Reapers, who are bent on destroying all organic life in the galaxy, would actually prove organic life to be useful and, thus, spare them from slaughter. However, Saren is clearly brainwashed, and the Reapers are liars.
In the sequel, Mordin Solus is responsible for engineering a new strain of the Genophage when it's learned that the Krogan are adapting to the original. However, though he considers it necessary, he refuses to ignore the true consequences of his actions and blindly accept that it was for the greater good. In fact, after he retired, he set up a free clinic in the slums of Omega to "do something less morally ambiguous."
His student, Maelon, regretted his actions in helping to create the genophage and tried to make a cure. However, doing this led to him working with the Blood Pack and experimenting on live Krogan.
Aresh counts as well. He wanted to restart the facility on Pragia, even after experiencing the torture that occurred there, because he felt that the work done there was done for a reason and should not go to waste. However, it's clearly a desperate coping strategy for dealing with his own childhood trauma, actually trying to put it into action would involve kidnapping and abusing even more children, an act that even Jack finds repulsive.
Warlord Okeer wanted to create the perfect Krogan to help his species. His reasoning was that Zerg Rush tactics did not work and would eventually bleed the populace dry, and he wanted the perfect Krogan as a Super Prototype for an elite group immune to the genophage, so that the Krogan would be strong again. Unfortunately, this led to him working with the Blue Suns and using any creations that did not fit his standards as cannon fodder
Her boss, the Shadow Broker, also qualifies. He tried to sell Shepard's body to the Collectors in the hopes that they and the Reapers would be pacified and spare the galaxy their wrath.
Shepard him/herself can be this as well. Depending on the actions s/he takes, s/he can end up sacrificing the Citadel Council to save human lives and increase human political influence, seizing and using Reaper technology made at the cost of hundreds of thousands of human lives to hopefully defeat the Reapers, leaving an autistic man in the care of his brother so that he can be used for experiments that will allow humanity to defeat the geth without a fight, sacrificing dozens of refinery workers to gain the loyalty of a member of his/her crew, sacrificing a member of his/her crew who'd trusted him/her to gain the loyalty of an even stronger person (Samara vs. Morinth), etc.
In the Arrival DLC, Shepard is given no choice but to blow up a Mass Relay to delay the Reapers' invasion of the galaxy. Said Relay takes out an entire solar system when it is destroyed, wiping out a colony of 300,000 people.
Of all things, the Reapers pull this to an extent. They think organic life is so weak and transient that by converting it into an immortal Reaper, they're doing it a favor. It grants an end to strife, disunity, and suffering, yes, but it requires being melted into a metal while still alive.
Luc in Suikoden III. If he succeeded in destroying the True Wind Rune, the grasslands would be destroyed, killing a million people. But, hey, if it keeps the True Runes from eventually letting humanity die off, and keeps the gray, stagnant world from happening, then it's good, right?
Tracer Tong from Deus Ex is one and you can choose to join him and ultimately destroy all global communication, thus plunging the world into a new Dark Age. He fancies this rather than the modern world with its perfidious and power-hungry secret societies, dehumanising technical innovations, and devastating artificial plagues (apparently, they are worse than the natural plagues that haunted the medieval world).
The Templars from the sequel abhor all front-edge technology, with nanoaugmentation being the worst of it all, and strive for a devout, theocratic society. If you help them establish one, they lynch you for being a receptacle of said infernal nanotech and for generally being of no use to them.
Ohmars - a faction of cyborgs with a Hive Mind regard themselves as the next stage of human evolution, and you can help them inherit the planet by removing all the other factions' leaders. The Ohmar then turn the world into a postapocalyptic, barren wasteland.
Actually, it's the remaining factions that ruin the world through 200 years of war. The Ohmar are just the only ones that survived after everyone else killed each other off.
Jedah Dohma from Darkstalkers believes that the best way to save civilization from destroying itself is to destroy the world and everything populating it, human, animal, and Darkstalker alike, and combine their souls into the body of an Eldritch Abomination that will rule over the new world as its god.
Vayne of Final Fantasy XII subjugated nation after nation, killing their ruling royal families/existing governments, murdered his own father, and leveled an entire city just to prove his weapons were working properly, all to free all life on the planet from the Occurians who have been pulling everybody's strings unnoticed for centuries, if not eons.
Admiral Aken Bosch of FreeSpace 2. He's the leader of a xenophobic rebellion of Terrans against their allies, the Vasudans, but his intent is to form a greater alliance between the Terrans and the Shivans, the xenocidal Starfish Aliens of the setting, using a pioneering new technology to communicate with them.
The Paragon Branka from Dragon Age: Origins wants to recover the Anvil of the Void — an artifact that can be used to create golems — in order to defeat the darkspawn and restore the dwarven empire to its former glory. When she discovered the Anvil lay at the end of a labyrinth full of deadly traps, however, she sacrificed her entire house and allowed her female followers to be transformed into broodmothers so that she could have an endless supply of darkspawn to test the traps.
Teyrn Loghain's betrayal can be interpreted as resulting from a desire to do what's best for Ferelden. After all, many of the Grey Wardens who died came from Orlais, a country he hates. Additionally, King Cailan refuses to listen to reason and decides to fight on the front lines against the darkspawn. Loghain originally only wanted to eliminate the Wardens, but if Cailan insists on fighting with them, then it may be beneficial to remove an ineffectual king. For the good of Ferelden, of course.
The Architect in The Calling novel wishes to end the constant struggle between the darkspawn and everyone else...by spreading the darkspawn taint to every living thing, turning everyone into half-darkspawn and killing the Old Gods. His methods are brutal. He will try to talk you into helping him, but if you then even consider changing your mind, he will kill you without a second thought.
The Grey Wardens themselves. They dedicate their life to fight the Blight, and they make it clear from the moment you join them that they (and therefore, you) will do anything that can further their goal. Examples of things you may have to do: interfere in dwarven politics and put a king in charge of Orzammar, in order for the dwarves to join you; overthrow and kill the current king of Fereldan, because he's against you (and a bastard, though); accept the obliteration of the Circle of Mages by Templars, in exchange of the latter helping you; killing a child possessed by a demon, in order to save a noble, and possibly, to get him on your side...The list goes on.
Anders in Dragon Age 2 has been possessed by a spirit of Justice, warped by anger into a force of vengeance, and is not above committing acts of terrorism such as blowing up the Kirkwall Chantry (cathedral) with the Grand Cleric (bishop) inside to remove any possibility of compromise and attain freedom for the mages of Thedas.
Merrill, as well. She has turned to blood magic and made a deal with a Pride Demon in order to repair a broken elven artifact and reclaim some of her people's history.
The Arishok is a prime example. He is convinced that all of Kirkwall is a cesspool that needs to be cleansed by forcing all bas (qunari word for "non-believer"; literally, "thing") to choose (that's right, a forced choice is still a choice, as far as the qunari are concerned) to follow the Qun, which imposes order on all followers. The scariest thing? He may be right, given Hawke's experiences in Kirkwall. However, he and the Qunari of Kirkwall merely keep to themselves and do not take action until the finale of the second act, and only because they've been pushed to their limits by the resident Smug Snake.
Purge from Space Channel 5 Part 2 is an 18 year old Psychopathic Manchild who believes that he's been given a holy mission to lead the entire galaxy, which he considers to be "Brutish and Unhappy", to the heavens.
MasterXehanort in Kingdom Hearts: Birth by Sleep is this. He feels that the World's (yes, it is capitalized) light and darkness are out of balance and seeks to forge the χ-blade to open Kingdom Hearts and create a new world where the two forces can be balanced once again. To that end, he almost killed one of his pupils after completely stripping his heart of all his darkness, and started another Keyblade War—the last one of which almost destroyed the World completely.
Though he Jumped Off The Slippery Slope. Hard. And speaking of Masters, we might as well mention Master Eraqus, who tried to kill Ven after finding out that Xehanort needs him to create the X-Blade, so all his plans can never come to fruition.
Are you sure that's what Xehanort's original goals were? It seems to me he just wanted to start another Keyblade War simply for the sake of curiosity. And obtaining the X-Blade was necessary to start another Keyblade War. Or did I misunderstand?
Valkyria Chronicles has the Atlantic Federation. Their goal is noble enough, in that they want to defeat The Empire while, at the same time, minimize the losses they and the independent Gallia suffer. Unfortunately, they attempt this by forcefully trying to take control of Gallia behind the scenes using very morally questionable means, including attempting to kidnap Archduchess Cordelia for ransom and, in the sequel, providing weapons and supplies for the Rebels.
Modern Warfare 2: General Shepherd orchestrated the events of the plot ("No Russian" and the subsequent invasion of the East Coast) because American had become gun-shy in the wake of what happened in the first game (the nuke that killed 30,000 Marines) and he wanted the nation to regain its standing.
Some of the villains in the Fable series have, or at least had, good intentions. Notably, Lucien from Fable II wanted to resurrect his family (although he jumps off the slippery slope and becomes a Complete Monster as the plot continues), and Logan from Fable III was driving the kingdom into the ground because he needed to raise enough money for an army to battle an Eldritch Abomination. As the series continues, it may well turn out that Theresa is a well-intentioned extremist, too.
The Moniter of Installation 04, 343 Guilty Spark, from Halo is a loyal and devoted servant to the Forerunners, doing what he is programmed to do even with them being extinct since 100,000 years ago. His primary goal is to put down the Flood so that they won't consume the galaxy, and he'll do everything to achieve it...and I mean everything. Even manipulating ignorant humans to activate the Halo rings, which would kill off every sentient being in the galaxy, just so that the Flood won't have any food sources left to feed on. And if any human refuses to activate the rings, then they're as much of an enemy to the galaxy as the Flood, and they must to be put down too...
PrinceEoniaTransbaal, from the Galaxy Angel gameverse, wants to use the power of the Lost Technology to expand the limits of the Transbaal Empire and increase the wealth and prosperity of its populace as a result. Even Tact Mayers admits that it is a noble goal. On the other hand, he has no qualms against committinggenocide in order to achieve said goal.
The Etrian Odyssey series regularly deals with these, with at least one showing up in each installment. In the third game, The Drowned City, the player's guild winds up caught between two Well Intentioned Factions: one has spent the last hundred years killing anyone who came too close to the Eldritch Abomination they've been keeping at bay, while the other wants to try and destroy said abomination, even though it feeds on negative emotion and might end up strengthened by the fear of everyone aware of its existence to the point where it can't be killed.
Lance from Epic Battle Fantasy, though only in the second game. After the destruction of Undead Goku in the first game, Lance gathers an unstoppable army and begins conquering the world, so the world can be united under one rule and world peace can exist.
Everyone in Nier. Nier himself wants to save his daughter...by any means necessary. Devola and Popola want to restore the dying world to its former splendor...by any means necessary. The Shadowlordwants to save his daughter...by any means necessary.
Nessiah of Yggdra Union, who has been manipulating a large chunk of the human population in order to gather the necessary magical power to free himself and go fight Asgard. Asgard is, by this point, everything a good dystopia ought to be—and has been this way since its creation, as a world of absolute order that takes a rather...militant approach to anything that seems to fall outside of its regulations, such as people like Nessiah, who was brutalized and exiled for protesting that he didn't want to fight and die in Ragnarok. The place also so happens to be run by series Big Bad Hector.
Gulcasa is also explicitly revealed to be one of these in Blaze Union. Life Isn't Fair, poverty is a serious problem, and innocent people are suffering everywhere. His solution to this supposedly unchangeable situation? Screw the system—if the world at large is Doing It Wrong, all he has to do is take the damn place over and run it himself. (And according to Yggdra Unison, the world really would be a better place with Gulcasa ruling it.)
Hans Tiedmann of Dead Space 2 used the player character's psychosis to build an Artifact of Doom, ordered looters on the Sprawl to be shot on sight, and attempted to hinder and kill Isaac multiple times throughout the game. Logs at the end, however, reveal that he genuinely thought that building Markers was needed for mankind's survival (suggested to be a form of Mindscrew that the Markers do to propagate themselves), had a legitimate sense of duty to the Sprawl's inhabitants, and disobeyed his superiors and ordered an evacuation when the Necromorph outbreak started.
Arguably, from Final Fantasy XI, Lady Lilith. Well, it's either her world or yours. Take a guess which one she wants to save. However, in the end, thanks to Atomos' Critical Existence Failure and the fact that she's going to die soon, she's the one who offers to Lilisette the way to save both futures.
The Garlean Empire from Final Fantasy XIV is hinted to be this as of now: there were various mentions by those brainwashed by the empire that their attempts at what could be comparable to Genocide, possible Deicide and the subjugation of various people, were done in order to prevent a catastrophic event from occurring on the planet.
In Sin and Punishment 2, the Nebulox/G5 want to kill Kachi as a suspected spy from Outer Space so that the humans on the new Earth will have more rights than before.
Johannes from Gods Eater Burst. It turns out that the Aegis Project, claimed to be mankind's last hope, is only capable of saving 1000 out of several million people. Despite this, Johannes continues with the project anyway, truly believing that it's the only way. He even seems aware of how evil he's become, as he refuses to be one of the 1000 saved, believing that he no longer deserves salvation.
Redwater from Dead To Rights: Retribution is honestly trying to rid Grant City of crime the best way he knows how. Unfortunately, this involves turning the city into a Police State and killing his longtime friend and partner, Frank, simply for getting too close to the truth.
Andrew Ryan in the first two BioShock videogames, in his own mind, probably had the best of intentions when he built Rapture as a sort of capitalist paradise, perceiving the outside world as morally bankrupt and parasite-infested. Unfortunately, his purely capitalist "paradise" had no rules, and everything went down the thunder bucket.
In Riddle School 5, this is what Viz amounts to. He tried to eradicate evil in the universe by attempting to destroy all the planets. He was just a little misguided about where to find said evil.
In Rosenkreuzstilette, Graf Michael Sepperin counts as this. He launched a coup against the Orthodox Chuch for good reasons; Number 1, to build a war for Magi to live in peace in, where they would be free of fear and persecution, and Number 2, to (supposedly) protect his biological daughter, Iris, whom the Church wanted dead. Of course, he didn't know that Iris was manipulating and deceiving himfor laughs.
In the third Dark Parables game, an evil artifact has persuaded the Snow Queen that following its directives will revive her son, who has spent the last few centuries in an enchanted sleep, and at this point, that's all that matters to her.
In BlazBlue, it is very easy to pin the NOL as some sort of The Empire, with their totalitarian, iron-fisted rule and their law of 'anyone not obeying our rules are to be executed'...until you realize that if NOL didn't put up such an iron-fisted rule, the Crapsack World will plunge into further chaos, with many dangerous Ars Magus free for people to claim, with a high possibility of the claimer being psychomaniacs out to destroy the world. It may be a cruel method, and the NOL look like jerks doing their job, but they do try to make the world a better place to live in. However, the reason why NOL is easy to pin as an unabashed evil empire is the fact that, possibly, the whole organization is being manipulated by not one, but two over-the-top Complete Monster with high Villain Sue caliber.
Doctor Proton is portrayed this way in The Doctor Who Cloned Me, the singleplayer DLC campaign for Duke Nukem Forever. While his ultimate goal (defeat the aliens) is good, his means to reach it (kill Duke Nukem, replace him with an army of Terminator-like robots who look like him and put one of them as a puppet president while being the Man Behind the Man, just to prove to himself that robots can be superior to humans) are certainly not.
Visual Novels
The Church in Tsukihime is portrayed this way. They can't go too overboard because they're supposed to be secret. The only reason they're not trying to kill Arcueid is because, well, she's essentially unkillable. They gave up. Supplementary materials indicate that they prefer the 'kill the evil non-human, burn the body, and cover up all the evidence' course of action, and ask questions only if they are unable to actually kill said non-human, as in the case with Arcueid, Ciel, or Wallachia.
Web Animation
The Big Bad of Broken Saints, Lear Dunham, goes to ridiculous extremes (the most disturbing of which involve the torture of his own daughter) to create a new world order that will set right all the wrongs of modern society.
Celesto Morgan in Dominic Deegan: Oracle for Hire. Compare him to the far more ruthless (and detestable) Knight Templar Raf Maliksh, who tries to kill Celesto for being insufficiently fanatical.
As shown somewhat earlier in the strip, Miranda West of The Wotch walks full stride into Well Intentioned Extremity in a recent arc, where she punishes Ivan for being too intrusive in his desire to discover Anne's secrets, also condemns two innocents, and then refuses Ivan's plea that he has (apparently) learned his lesson, as well as refusing to help the ones who had nothing to do with her concerns, threatening him when he calls her out on it. But her status as a Well-Intentioned Extremist comes not just from her actions, but also from her attempt to justify it to her familiar (and herself).
Another example: Professor Broadshouders in Zebra Girl has made it his life's mission to rid the world of demons - and doesn't care who he has to hurt, damn, or kill to get the job done.
Up to and including himself.
Baron Klaus Wulfenbach in Girl Genius rules with an iron fist to protect the world from the sociopathic, unwittingly violent genius of the "Sparks". Attempts are made to paint him as a Necessarily Evil ruler whose methods are indeed improving the world, though; it is stated a few times that Klaus doesn't enjoy babysitting Europe.
Klaus is actually an extremely interesting example as he could actually be called a "reluctant tyrant". He hates his job, and would much rather be off adventuring or making crazy inventions (he rarely gets to partake in the latter). As a dictator, his rule basically comes down to "Don't make me come over there!" (Don't start a war, or tamper with forbidden technology of the Other.) Don't break that rule (or make a move to do so), and he is quite content to leave people alone.
Othar Tryggvassen, Gentleman Adventurer!, from the same series. He plans to kill every Spark in the world, ending with himself, due to the sorry state Sparks have left the normal folks of Europa in. This may explain why people keep throwing him out of airships.
Pretty much EVERY Spark (who isn't already a full-time villain) is, at one time or another, one of these. It goes with the Sparkiness. Even Agatha. As demonstrated here.
In Kid Radd, GI Guy believes that humans and sprites are too far predisposed to hurting each other to hope for peaceful existence, and that a mercy-genocide is in order to stop the suffering.
Radd: He was just... well, like a lot of madmen. Somewhat accurate view of the problem, really insane view of the solution.
Redcloak from The Order of the Stick, if one reads Start of Darkness, falls squarely into this. He wants to improve life for the goblinoid races, but attempts to do so by putting down the other humanoids via divine blackmail, instead of by actually helping the goblins improve their lot.
Even more so, Miko Miyazaki from the same strip. A case study in what Lawful Good can do, when taken to its extremes. Justice untempered with Mercy, blind to the possibility that she could ever be wrong.
On the heroic side, Vaarsivuus is getting there as well in recent comics. At this rate, (s)he'll end up like Belkar...
However, Faye, Dora, and Marten then quickly point out how wrong this is by asking her what she'd think if a mandid what she did to women who mistreat their boyfriends. She'd ask him out. And then she orders her Vespa-bot to shoot Dora and Faye, with the lasers set to "disfigure".
Ian Samael from Errant Story comes from a culture where Elven oppression is common and many Elves wouldn't think twice before wiping him out. His goal to keep his people from being hunted down by Elves is fine; pity that he tries to do so by attempting to wipe out the Elves himself.
Darkbringer from Lightbringer strongly believes that the only way to fight evil is to embrace its ways, abandon all hope, and give up himself to darkness and despair. He believes that Lightbringer's actions give people false hope, so he wants to kill him.
SUEPR Team One, from City of Reality, attempts to protect Reality's Mary Sue Topia by destroying the entirety of the neighboring World of Magic, which has threatened to wreck their way of life. The protagonists are forced to try to stop them, despite nearly falling victim to the very same cynicism.
Weijuaru of Juathuur basically wants to make every juathuur a god, because that would mean absolute freedom.
The robot Blunt in Freefall. Just wants to protect humanity...and has no problems with a plan to lobotomise millions of robots to remove the chance that any of them could harm a human.
Lenny Priestly of Survival of the Fittest V3 has shown that he would do anything to get his sister off the island, including killing his classmates. May be subverted; there are some implications that he may be using her as an excuse to go on a killing spree, especially now that he's gone all Ax Crazy and lost his Anti-Villain status...
Rachel Gettys from V4 is also one.
Aaron. Hughes. Yes, he's trying to find a way off the island. However, his methods are rather...extreme. At one point, he flat-out acknowledges to himself that he doesn't care if his allies get killed, just if the majority of the class gets off the island. That's not getting into his Manipulative Bastard tendencies, or how, previously, he had let one of his former friends be killed just so he could portray him as a martyr to the rest of his group. Or the fact that he manipulated another character into electrocuting someone to death, simply because both characters involved were "a threat".
Dr. Horrible. At least, in the beginning, if you believe him. He tries to convince himself that this is still the case during the "Slipping" song, probably unsuccessfully.
Dr. Horrible: Then I win, then I get everything I ever/All the cash, all the fame and social change/Anarchy, that I run!
His fish metaphor when he first speaks with Penny is another good example.
Dudley Griffin of KateModern is one of the few people prepared to confront the Order head on. Pity he's such a violent jerk.
Dr Stee wants to make the world a better place (for himself), a "Utopian Playland", by taking it over - with giant robots if necessary - and becoming World Emperor.
Brother Joseph: Y'see, these are good people who try their best to raise their children who aren't corrupted by the lust for dominance that the outside worships. But for every group of good people, there needs to be an evil man who keeps that knowledge of how tempting it can be. And I AM that evil man.
Dr. Diabolik of the Whateley Universe. He's dedicated to making humanity better, and he's found a way to 'awaken' hundreds, if not thousands, of people at a time. It involves raiding an entire medium-sized city and doing things that unfortunately cause the deaths of maybe hundreds each time. He also turns a profit on the deal, so he can afford to keep doing it.
Lord Doom has a plan to save humanity from overpopulation, hunger, crime, war, and tyranny. His plan promotes universal literacy, tolerance for other ethnicities, political creeds, and sexual orientations, grant universal health care for all, and generally make life more pleasant for everyone, as long as you didn't mind giving up a couple of small, tiny, insignificant things in the meantime...things like a right to vote, or freedom of speech, or the right to choose your own occupation. Small things like that. Oh, and he's in charge. Forever.
Lord Vyce wanted to save the multiverse from 'The Entity', so he goes around protecting other universes by conquering and enslaving them.
In The Gmod Idiot Box, DasBoSchitt's way of defending Renamon from people who portray her in a pornographic manner is to repeatedly kill her and portray her in other ways (such as attacking Duke Nukem) to make these people hate her, and, as a result, has been repeatedly viewed as a Renamon hater, or even a furry hater.
The fanatic but charismatic Jet, a guerrilla freedom fighter on Avatar The Last Airbender from mid-Season 1, who reappeared near the end of Season 2 with the intention of redeeming himself only to discover that Redemption Equals Death.
Katara starts veering into this territory late into the series, being willing to do more and more extreme things to save the world. Not to mention her constant complaining about the Gaang accepting the help of the recently Heel Face Turned Zuko. She gets better eventually, though.
Long Feng arguably comes off as this at first, with all his talk of preserving culture and avoiding panic, but by the end of his arc, it's clear that the extremism has overshadowed the intent enough to place him firmly in the villain category.
Pixar has some examples - Pete Docter, director of Up and Monsters, Inc., even said that he thinks a true villain ("I'm gonna wake up and do evil!") is an unrealistic character.
Waternoose from Monsters, Inc. is a father-like figure to Sulley and, his motto "We Scare because we Care" is genuine, as he really does wish to maintain the Monster World through providing energy from children's screams. So, to this ends, he builds a horrifying machine that will suck the screams out of children and, as he says to Sulley, is willing to "kidnap a THOUSAND children before he lets the company die...and silence anyone who gets in my way!"
WALL•E's AUTO, the autopilot of the Axiom, refuses to let the inhabitants go back to Earth, even though this directive is more than 700 years old and plant life does exist (as shown at the end). But hey, he's a computer. He can't choose not to follow his programming. He's not so much a crazy AI as just following an ill-considered directive by a man seven centuries dead. Besides, realistically speaking, one healthy plant does not promise enough resources for the entire population of that huge ship.
Which is another reason why Pixar decided to add that lengthy musical montage as the coda.
Pixar added the final montage because, without it, test screeners debated whether humanity actually survives or only lasts a few weeks, which would have turned WALL-E, EVE, and Captain McCrea themselves into good examples of this trope. Word Of God established humanity's re-flowering on Earth as well as the re-flowering of Earth's ecosystem, thus averting any interpretations of the adorable WALL-E actually being a cruelly selfish individual who drives humanity to extinction just to be with his girl.
Charles Muntz from Up just wants to catch a bird and prove that he was right. Unfortunately, his methods (after going completely crazy) include killing everybody who shows up at his refuge.
Equinox in Batman The Brave And The Bold. He wants to balance Chaos and Order BY DESTROYING AND RESETTING THE UNIVERSE.
Kr'ull the Eternal simply wants to have an empire that won't age and die while he has to watch it suffer. He plans to replace all the humans in the world with eternal bodybuilders just like him. By the 25th century, he seems to have gotten over it.
Sideshow Bob: Because you need me, Springfield. Your guilty conscience may force you to vote Democratic, but deep down inside you secretly long for a cold-hearted Republican to lower taxes, brutalize criminals, and rule you like a king. That's why I did this: to protect you from yourselves.
Similarly, the episode "Sideshow Bob's Last Gleaming". Certainly, Bob claimed that he was doing a good deed by ridding Springfield of TV, but all it really did was make him the top dog in the manger.
Also, when Bob sees Springfield give into his demands, he exclaims "I should have made more demands!"
Bob's not the only one to utilize this trope: Jimbo Jones often steals dolls because he believes that they would harm girls. Even Bart Simpson has had shades of this. One particular example had Bart gaining increased intelligence from a drug, but then seemingly growing insane and beginning to believe that the MLB was spying on the town. He then went as far hijacking a tank from a military base, driving it across Springfield, and stopping in front of Springfield Elementary, and then proceeding to fire into the sky (after several tense moments where Bart periodically stopped the cannon on various locations [specifically, Springfield Elementary, The First Church of Springfield, and the Frame Shop, respectively]), shooting down the satellite, all in order to prove that he was indeed telling the truth and was certainly not crazy (well, for the most part).
Homer also had shades of this. One notable instance of this is when he decided to go all The Grinch on people on Christmas and steal gifts, because he legitimately believed that doing so would result in people actually caring for each other rather than focusing on themselves. Unfortunately for him, it backfired, resulting in the town hating him afterwards.
Marge exhibits at least one moment of this when she rallies to have all sweets banned from Springfield under "Marge's Law", leading to a bootlegging operation in which Homer himself is involved.
Mayor Quimby, the town's resident Corrupt Politician, also showcased shades of this. In one episode, he declared a 75 cent tax on the highway, and after people started evading it, tried to force people to go through the checkpoint. Why? Because he needed the tax money so that he could de-python the town fountain (which, as the phrase implies, means that the town fountain somehow got pythons in it, causing a panic when it sprays snakes instead of water, causing the occupants to leave). Another instance was when he tried to prohibit alcohol on St. Patrick's Day to reduce the potential amount of riots that would occur from being drunk, but it backfired when Irish Catholics and Irish Protestants were unable to put aside their differences without alcohol, and resulted in them still getting into a riot anyway.
Mr. Burns also sometimes has this as his motivation for some of his bad actions in some episodes: a particularly notable example was when he tried to ruin the Power Plant's union in "Last Exit to Springfield". The reason he felt that he should eliminate them was because he realized that it was becoming inherently corrupt, remembering what a worker his grandfather had dragged off had said, and wanted to destroy said corruption one way or another.
Agent Bishop from the second Teenage Mutant Ninja Turtles animated series has one mission: to protect Earth from alien invasion. In order to achieve this, he has used aliens as unwilling test subjects for genetics experiments, faked an alien invasion and kidnapped the President in a ploy to guarantee funding for his agency, the Earth Protection Force, attempted to produce a sleeper army of super-soldiers to covertly kill people suspected of being aliens, and, ironically, prolonged an alien invasion in order to fulfill the terms of an agreement with yet another group of aliens. Eventually, however, deciding that diplomacy is a more long-lasting and effective way of protecting Earth, he gives up Black Ops.
In almost all incarnations of Transformers, Megatron is forced to become one of these because Decepticons were second-class citizens due to an earlier war. That is, of course, his only redeeming quality and it isn't a very good one.
Well, some of them are nice guys to those troops that don't betray them, and name Prime a "worthy opponent".
And note that, despite being "the bad guys", not all Decepticons are inherently evil. Many of them are just soldiers doing their jobs, and it's hardly their fault that the side they picked happened to have attracted the most psychos.
In Beast Machines, Megatron has a seemingly good idea, in principle. He wants to eliminate political squabbling, which results in nothing ever getting done, by uniting all machines under one mind. Of course, there are problems with this - Megatron is egomaniacal, wanting his mind to be the one in charge, sacrificing the minds of others and destroying those who would stand in his way (the Maximals). Also, he wants a purely technological world, eliminating all organic races.
Nerissa, the main villain from W.I.T.C.H., used to be one of the good guys in charge of protecting the universe, but soon realized that the only way to truly protect the universe was to bring it under her rule, so that she could ensure that there would be no war, suffering, or injustice. For the most part, she ensured that no innocent people were harmed in her crusade, aside from the heroes who opposed her.
Nerissa is...debatable. The reason she is a former good guy is that she accidentally killed her friend Cassidy when she was given the Heart of Candracar after it was taken from Nerissa. It's also implied that she murdered the one person who took pity on her after escaping her prison, and impersonated her so that she could have a child to lead the rebellion against Phobos so she could steal Elyon's power. And she killed a living clone of one of the heroes she created. And she targeted their families with a monster that feeds on the hate of his enemies who was created from the boyfriend of the same heroine she cloned, who was also her successor as the Keeper of the Heart). Several of her attacks on Meridian and Zambala specifically target civilians to obtain Hearts, or just because she's vindictive and/or high on her power. By the end of the series, no one is buying her sob stories and knows that, for Nerissa, It's All About Me.
Æon Flux's nemesis Trevor Goodchild honestly believes that by walling off his entire country, placing surveillance cameras everywhere, and conducting bizarre experiments in psychology and genetics, he's providing an unobjectionably safe existence for his subjects and gradually improving their quality of life. The frightening thing about this show is that, half the time, you suspect he may be right...
Examples of this trope often turned up as villains/antagonists on Superfriends.
Including one villain who thought that it was such a CRIME to spend money on space exploration instead of helping the poor...as opposed to shrinking a whole space center and kidnapping everyone inside?
Word of God claims that this is the way the Brain from Pinky and the Brain should be viewed. He wants to rule the world not for the sake of being a dictator, like his rival Snowball, but because he believes that he could do a much better job of it than the people currently in charge.
Charlie Dog from Looney Tunes. Poor guy, all he wants is to be loved but he goes at it so wrong...
Rameses the Pharaoh from The Prince of Egypt. Rather than making him a cardboard cut-out villain, the creators wrote him as a "Well Done, Son" Guy with a Freudian Excuse who has a very close relationship with Moses (they grew up together as brothers), who's just doing what he feels is right for the country and his dynasty. His father is the same, and even gives a little speech about how it is necessary to make sacrifices for the greater good (the "sacrifice" being the mass-murder of children). Of course, neither of them feel particularly guilty about ordering the massacre of slaves.
Ra's Al Ghul, who barely manages to scrape into the "well-intentioned" category. His rather vaguely-defined motive is to restore the Earth to it's original, "pristine" state. His method is wiping out half of humanity.
Catwoman probably also counts. Her goal: to collect funds for wildlife preservation. Her method for achieving this goal: dress up as a ninja kitty and raid jewelry boxes.
Mister Freeze is introduced as one of the "Revenge at any cost" variety, out to avenge himself on the Corrupt Corporate Executive who pulled the plug on the research he hoped to use to save his wife's life and caused the resulting Freak Lab Accident that made him what he is.
Magneto of Wolverine and the X-Men sees himself as closer to this than Knight Templar, but considering his plan...well, it's probably closer to the latter in the eyes of others.
Magneto's depiction in the 90s X-Men cartoon also qualifies. When Xavier questions his ideas, Magneto states that attempting to go with reason against an enemy using force led to it getting crushed.
The Avenger's: Earth's Mightiest Heroes has Kang the Conqueror. The future where he comes from is being erased from existence, so he goes to the past to fix this. He decided that the best way to do this is to conquer the past to prepare the people of earth for the coming Alien Invasion.
Dante's Inferno: An Animated Epic - Dante, before and during his time in the crusades. His unquestioning loyalty in his religious mission causes him to justify the beating of a prisoner for protecting a woman by claiming that he deserved what he got for being a heretic. He also uses his status as a soldier of god to gain comfort from the women whom the beaten prisoner was protecting, despite promising his wife that he would remain true to their marriage.
Soldier: "Dante, do not commit this wicked sin!" Dante: "How is it a sin, if I'm already absolved?"
SpongeBob SquarePants: Mr. Krabs wants to prevent Plankton from taking over the world: by driving him to suicide using his fear of whales.
The National Security Agency of The Zeta Project veer in and out of this trope. They exist to take down high tech terrorists and threats to human life, basically serving as the FBI and CIA of their universe. However, they themselves have had a lot of morally gray moments. Allowing a mad bomber to kill people because he'd get a terrorist they were after in the process, for instance, along with a lot of human rights violations all over the place. You have no right to a trial, they do not need a search warrant, they can detain you against your will, you do not have the right to an attorney when interrogated, and they carry weapons that are a lot more vicious and brutal than bullets. The zigzagging trope part comes in when they're proven to be completely right half the time and, as a part of the DCAU, they've faced end of the world scenarios before.
On South Park this usedto be the schtick of Kyle's mom, Shelia, whose parenting was always played Up to Eleven, reaching its zenith in the movie.
In the 1930s MGM cartoon "Jitterbug Follies", Count Screwloose tries to scam the public by selling tickets for a show that won't go on, but a group called "Citizens For Fair Play" tell him to put on a show or else. They happen to to act and dress like 30s-style thugs.
