Elfen Lied: Nozomi's father only attempted to prevent her from realizing her dream of becoming a singer because she suffered a throat defect that may cause her to lose her voice, the very same kind that her mother suffered from and which eventually drove her mother to suicide. Unfortunately, his methods of preventing her involved physical abuse, which left Nozomi with self-esteem issues and a bladder control problem, at least until she asserted herself about her dreams. It also doesn't help that there were also other alternatives instead of abusing her, yet he ultimately turns out to be right as Nozomi indeed loses her voice towards the end of the series.
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).
The Hero is Overpowered but Overly Cautious: The residents of the Dragon Village want to sacrifice Elulu to create the holy sword Igzasion, all to defeat Gaeabrande's Demon Lord. They'll go as far as to slip the party paralytic drugs to ensure that they can't interfere with the ritual. They also killed any of their citizens who opposed the sacrifice, including Elulu and Mash's families.
I Wish: Dee comes across as this. Since she's a witch, she studies like crazy to improve her abilities in repeated attempts to help make the world a better place for people. Unfortunately, her hyper and rather carefree attitude about her powers often leads to her magic failing or ultimately making things worse. While she wants to help K by having him experience love through a Love Potion, she tried it on all of her servants first and it resulted in them becoming obsessed with her, to the point that they'll kill her. Fortunately, once Wye goes through a convoluted plan to get himself temporarily killed and Dee's powers become better, Dee learns the lesson that using her magic can cause severe consequences and she isn't as carefree about it anymore.
Stain, the hero-killer, targets only the heroes that he feels are acting only in their self-interest because he idolizes "real" heroes, those who act selflessly and for the sake of right as opposed to for fortune or fame, such as All Might. It's even stated that he tried to become a legit hero before becoming disillusioned with the scene and turning to darker methods to enforce his ideals of justice. However, what constitutes as "self-interest" to him includes even those genuinely heroic ones who do it because they see it as a family occupation or as a way to make money for their struggling loved ones, which is just as worthy as death to him.
There is a number of well-intentioned extremists in Code Geass.
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 making his beloved half-sister go Ax-Crazy, so Lelouch had to kill her and make the best out of a bad situation. In all, he often has a choice between a terrible, terrible thing, and an even more terrible thing.
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.
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 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 and his own sister Nunnally as pawns.
Even Nunnally, of all people, 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 plan to use nukes, but she just couldn't stop Schneizel, who had been using her. 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.
Both of them were Char Aznable 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
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 with 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).
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.
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 Redemption Equals Death.
Gundam 00's 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. It was all The Plan by Schenberg to unite humanity in order to prepare them against an Alien Invasion.
All Ryoko Asakura 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.
Lordgenome a brutal though world-weary dictator who was the only thing preventing his masters from wiping out his species.
The Anti-Spirals 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: Sometimes the best intentions can lead us down the wrong path.
Finally, at least from the viewpoint of the four 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.
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'. 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. 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.
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 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).
The majority of Naruto villains fall under this trope, though the lengths they're willing to go to in the name of "peace" are usually completely ridiculous:
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 seems to qualify. 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. Many of the problems that are being faced, including Nagato and Kabuto going bad, are his fault. The Uchiha rebellion attempt is partially his fault as well. The reason why he doesn't fully qualify? Aside from his stated reasons for why he did what he did, he apparently was also jealous of Sarutobi Hiruzen, being Always Second Best to the one that became the Third Hokage. In essence, he went to the lengths he went to show he wasn't as soft as his chosen rival, and his actions backfired hard on both himself and the Leaf Village, because he would always take the most extreme measure as a first choice of action instead of trying more peaceful alternatives that might work first.
Predating Danzo was Tobirama Senju, the second Hokage. He was paranoid and mistrusting of the Uchiha clan since childhood, disagreed with his brother's efforts to try to make peace with them, and enforced their isolation to protect the rest of the villagers after Madara tried to destroy the Leaf, disregarding that Madara betrayed his own clan to do what he did, and then claimed he didn't hate all of them, as a few earned his trust, while doing absolutely nothing to reach out to the rest of them like his brother would have. His actions and choices towards the Uchiha, however, helped catalyze their future mistrust of the Leaf Village Government, as part of the reason why the coup was happening was because of a perceived nepotism towards anyone with a direct link to the Senju Clan in some manner. He also developed the Impure World Resurrection that allowed Orochimaru and Kabuto to revive dead ninja to use as weapons, with the caveat that captured enemies would be used to bring back fallen allies. His rampant bigotry and paranoia towards the Uchiha, and the fact that he crossed a line in creating a means to revive the dead to use as weapons, and suddenly one understands why his own brother wanted to pass him over in favor of Madara, at least, before Madara turned on the Village.
Itachi is another example. He killed off his entire clan (save his brother), but it turns out he was under orders to do so because they were about to start a civil war. Had this happened, even more people would die and it could very well have led to a world war. He also joined Akatsuki, but this was simply to keep an eye on them and keep them away from Konoha as long as possible.
Tobi and Madara can also be considered this, since their ultimate goal is to end the current world and create a new one with no wars. Chapter 678 reveals that Madara does genuinely believe himself to be the savior of mankind, and was unaware of the Jubi's Life Drinker abilities. Moments later, he's backstabbed on both figurative and literal levels by Black Zetsu.
In chapter 692, Sasuke reveals he wants to remove from the world everything that led to the just-passed crisis and start over completely, which means killing the Five Kages and controlling the Tailed Beasts.
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...
Aureolus Izzard, who isolated himself three years ago after failing to save Index from having to have her memories erased to supposedly prolong her life and has been desperately trying to find a cure ever since. However, his plan involves manipulating many innocents with no regard to if they get hurt or killed in the process plus turning Index into a vampire, and his sanity takes a hit when he learns that not only has Index already been saved from this fate by Touma, but his method wouldn't have worked anyways since Index's condition was caused by the Lola Stuart's manipulations, not by any natural consequence of her grimoires like he thought, which causes him to just start trying to kill people in a rage.
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 and killed them in such brutal fashion in the faint hopes that the memories shared by the Hive Mind would cause the next Sister to refuse to fight him.
Fiamma of the Right, who wishes to save the world through a sort of forced purification. Touma acknowledges Fiamma's basic goal as being a good one, but condemns his extremely destructive methods and his disdain for individual lives.
From the spin-off A Certain Scientific 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, Meruem, the Chimera Ant King, suddenly makes a dramatic change into becoming a Well-Intentioned Extremist from wanting 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 Chimera 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.
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.
Elite Four Lance in Pokémon Adventures. 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 Adventures' R/S arc had the same ambition in the manga as they did in the games. 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.
In Future Diary, various people are chosen to participate in a battle royale, with the winner becoming God of Time and Space. They all need to do some pretty messed up stuff to succeed in this goal: even the protagonist, who starts out as The Woobie, ends up doing things such as slaughtering an entire orphanage and killing his best friends, which he justifies by promising to use his God powers to bring everyone he killed back to life once he wins the game. Unfortunately, bringing people back from the dead is one of the few things that a god can't do. Even then, the alternative would be to let the current god die of old age, which would result in all causality falling apart.
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.
The truly faithful Father Pucci of Stone Ocean, 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.
Funny Valentine from Steel Ball Run also qualifies. His motivation for gathering the Corpse Parts was so he could use them in conjunction with his Stand D4C to deflect any misfortunes that might have befallen America elsewhere, thus ensuring an everlasting golden age for his nation.
Kuze is a complete Anti-Villain and 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, trying to kill the rather well-meaning 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.
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!).
The balance of souls between worlds is so critical disruption can destroy existence itself. 200 years ago, the Quincies were so zealously trying to protect humanity from hollows that they destroyed too many souls and refused to listen to shinigami warnings. The shinigami were forced to go to the same extreme by wiping out the Quincies to save existence itself. The Ishida Quincies agree the shinigami did the right thing. The Vandenreich Quincies disagree. When they try to disrupt the balance of souls again, Mayuri is forced to kill 28,000 Rukongai subjects to correct it. Yamamoto says Soul Society would have supported Mayuri's act but he's angry that Mayuri didn't clear the bureaucratic red tape first before doing it.
The major Arc Villain of the Captain Amagai filler arc turns out to have been motivated by an attempt to correct a perceived family wrong. Captain Amagai was trying to avenge his father who had been killed by Yamamoto when he was a child. He didn't realise what his father had done, or why Yamamoto was forced to kill him, until it's too late for him to do anything other than take his own life in atonement for his mistaken vengeance.
Ichigo's inner hollow legitimately does want Ichigo to survive, but he'll go to any lengths to ensure Ichigo's survival - even if it means usurping Ichigo's body and turning him into a hollow with no moral restraints. This is why he appears whenever Ichigo is close to dying and whenever he grows stronger when Ichigo despairs — he grows stronger to eliminate the source of that despair. The "well-intentioned" part is best emphasized when the merged form of Hollow Ichigo and Zangetsu begins to cry after teaching Ichigo the Final Getsuga Tenshou, knowing that when Ichigo uses it, they will never see each other again — ultimately, the Inner Hollow has only ever wanted to protect Ichigo.
It turns out that Gin Ichimaru is this or at least, this is how he started although he deliberately cultivates the image of a Noble Demon. His motive is something the protagonists could sympathise with and support but the methods he's willing to (and does) use put him well outside the hero scale and firmly in the anti-villain scale. His methods are very extreme and drag him towards the Noble Demon he claims to be.
Old Man Zangetsu is revealed to be this in the final arc. It turns out that he's actually a personification of Ichigo's Quincy powers, taking the image of Yhwach as he appeared 1000 years prior, and had been trying to slow Ichigo's potential growth as a Soul Reaper and take his Hollow/Zanpakuto's place as his core powers. Why would he do this? To protect Ichigo from the inevitable fights and dangers he would face if he became a Soul Reaper. And for additional points, he'd originally intended to kill Ichigo if he were to become a Soul Reaper. Thank goodness he changed his mind.
Most of the villains from Getter Robo, curious for a classic Super Robot 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.
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.
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. 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. Kurt Godel also claims to be trying to save the world by keeping Fate from destroying it. And it turns out that Fate and Kurt 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 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.
Neo Saiba's goal in Digimon V-Tamer 01 is to create a world where no one can be hurt. His way of going about this involves a massive army of demons enhanced by the data of a genetic abomination, and the destruction of the Digimon World down to its base elements (0's and 1's).
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 HeelFace 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 HeelFace 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.
Rex Godwin, 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.
Kaito probably qualifies in the first season. He doesn't particularly like what he does to the people who he takes Numbers from, but he does it in order to heal his younger brother. Even Yuma respects him for this, despite the fact that Kaito never lets Yuma forget that he is on his "hit list". To make this worse, what Kaito was doing in the first season wasn't helping Haruto at all; it was a lie used by Dr. Faker, who was being manipulated by Barian in order to destroy the Astral World.
In fact, Dr. Faker himself falls into this category, but we don't find out until the end of the first season. For all his ranting like an Axe-CrazyMad Scientist who wanted to Take Over the World, his true goal was simply to find a cure for Haurto. His mistake, it seemed, was trusting the Barians and letting them manipulate him, forcing him to commit horrible crimes in exchange for promises they never planned to keep.
Actually, Zexal is full of this Trope. Elphias is willing to commit genocide on the Barian World in order to protect the Astral World, while the Barians are willing to do the same thing to the inhabitants of the Astral World to protect their people. (Except for Vector; he clearly doesn't even have good intentions.)
Then there's Mr. Heartland, who claims he's this, even quoting the quote on the main page by Bernard of Clairvaux nearly word-for-word before his duel with Kaito in the second season (cut from the dub); however, given his actions, it's very hard to believe he has any intentions for what he does except greed.
Jellal Fernandes 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.
Ultear is another example, though she ironically first becomes this type of character after her HeelFace Turn. For example, she doesn't at all have qualms with inflicting the Fairy Tail members lots of physical pain so they can awake their Second Origin and become stronger. Later, she genuinely considers killing Rogue who had done nothing wrong, because she knows that he will turn evil in the future and she wants to prevent that. However, she has a Heel Realization and doesn't do it in the end.
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.
Inverted with the Black Lotus Syndicate. They do things like establish orphanages and give aid to the poor...in order to cause overpopulation and drive mankind to self-destruction. This ends up driving Sentinel II into becoming a straight example, burning orphanages and the like for the greater good.
Kyubey in the original anime. What it's trying to do is avert, or at least delay, the heat death of the universe. Doing this just happens to involve turning young girls into The Heartless by driving them 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 Magical Girl if she agrees to it (though Kyubey almost never reveals all the details even after the agreement is made).
Paul von Oberstein in Legend of Galactic Heroes is a well-intentioned revolutionary with no moral borders whatsoever. He won't even blanche at such tasks as to allow the whole planet get nuked into oblivion for propaganda purposes. The most disturbing thing is that his ideas all work.
Guy from Ai no Kusabi. In order to remove the Pet Ring that binds his ex-lover Riki as a sex slave to Iason, he cuts off Riki's penis where the ring was attached. He then attempts to murder the aristocratic Iason to free Riki once and for all.
The Space Defense Force from Planetes were essentially space terrorists. They consisted of people from various nations that didn't have sufficient space-faring technology, and therefore fell behind while other nations that had a presence in space continued to get richer due to being able to exploit the resources out there such as from asteroids. Their main objective was to ensure that poorer nations got to benefit from technology and resources found in space, since many of them were suffering from civil war or lawlessness. And they tried several different methods to convince said nations to accept their demands, such as blowing up a space station or later, crashing a colony onto a moon base.
Ratchet: I'm sorry, but, we must bring an end to this meaningless waste of time, Orihime.
The main villain of Tales of Vesperia: The First Strike is, believe it or not, Garista Luodur, the Imperial Knights' best strategist, who wanted to create a new type of blastia that could help the people gain full control of Aer. To do so, he created a gigantic blastia within the abandoned castle ruins and wanted to test out his own blastias. There was a negative side effect to this, though; the blastias he created and tested out produced abnormal amounts of red Aer, which turned the leaves on the trees unseasonably red and caused the resident animals and monsters of the forest to go berserk and threaten the people of different towns. None of the knights knew Garista was behind it all, of course, but Yuri and Flynn finally figured it out near the film's climax and had to attack him for the safety of the others.
Played with in Bokurano. Dung Beetle and Kokopelli enlist 15 kids to pilot a giant Robot named Zearth, which kills its pilot after a fight, just to give our universe a chance to fight for its own survival... at the expense of 15 kids, 328 trillion human lives and 32767 alternate universes! It doesn't get better by the fact that one of the originally enlisted kids wasn't even born yet!
The titular character from Tiger Mask starts out as one. His goal is to defend the orphanage he grew up into, and, later, help all orphans of Japan. At the start, his method is to play the Foreign Wrestling Heel (and at one point skipping the 'foreign' part by coming back to Japan), beat the crap out of non-Japanese wrestlers (possibly other heels) and even main them, and provoke the public to hate him, so they'll pay to see his matches hoping to see him defeated. The series is both about him rebelling against Tiger's Cave (the organization that trained him and others and forces them to be the most violent heels around and pay half their money to them) and outgrowing his role as an heel and fighting fair without getting back to be a true heel.
Fifth Sector from Inazuma Eleven Go, an organization that own and controls soccer (primarily middle school soccer apparently) and wants to make sure that everyone, no matter who they are, can experience the joy of playing and winning at soccer and won't be put down based on their lack of soccer skills. They do this by fixing almost all matches with pre-determined scorelines, forcing teams to comply to these score-lines, and, on a best case scenario, closing down soccer clubs that don't comply, while on a worst case scenario, flat-out destroying any school who's soccer club doesn't go along with them. On top of this, they treat the entire thing like some sort of empire, and even call their leader, the one who "holds soccer in their hands", "The Holy Emperor".
Hyoubu Kyousuke from The Unlimited has has been betrayed many times by humans. He wants to create a world where espers could live in peace, but doing so would mean killing all "normals", thing Hyoubu will do without any hesitation.
A much more child-friendly version has Mamuu of Pretty Cure All Stars 3: Friends Forever. The mother of the tapir Yumeta, her only desire is to make her son happy. She does so by keeping children trapped in the dream world so Yumeta is happy forever. It takes the active Cures of that point of time to get it through her head that she's doing more harm than good.
Tarta and Tatra, the twin princesses of Chizeta in Magic Knight Rayearth. While they do invade Cephiro and try to conquer it, it's established that they only did so because their kingdom has gotten so overpopulated that they need more space. When questioned, Tatra even outright says that they have no desire to oppress Cephiro's natives.
Super Dimension Fortress Macross: Bodol Zer, commander of the Zentraedi, attacked Earth with a devastating Orbital Bombardment and tried to destroy the troops that were previously fighting against Mankind when he was notified said troops were negotiating a ceasefire. His reasons aren't clearly stated in the original series, but Macross 7 shows that the frontline troops' actions looked suspiciously like the result of a Protodeviln awakening, and given that the last time that happened the galaxy-spanning empire that had created the Zentraedi self-destructed to seal them away, destroying the planet and killing everyone involved was the only intelligent thing to do.
This series offers a different view for Dolza's actions: it's just that one million warships with incredible firepower are negotiating a ceasefire without informing him, and Dolza's reaction to the apparent desertion of such a force was to strike first before it could disperse and do god knows what.
The current Robotech Masters. Successors to terrible tyrants, they're now trying to save their civilization by recovering the last known supply of Protoculture, located on Earth, before the Invid or the Disciples of Zor come, and are genuinely puzzled by the Human hostility (to be fair, the high command of Earth wanted to negotiate, but before they could actually try and talk a trigger-happy officer fired nukes at them). Once the fighting started, however, they showed no compulsion against killing thousands of Humans nor willingness to explain their actions, and when they saw the Invid had found out of the Protoculture they grew desperate enough to demand the complete evacuation of Earth on pain of extermination and use their own civilians as brainwashed infantry;
Supreme commander Leonard of the Army of the Southern Cross is a known hardliner (even if not as much as his superiors) and a borderline General Ripper, keeping secret the fact the Robotech Masters' troops are actually sentients and not biological robots, actually being the last surviving leader of the Anti-Unification League, and generally acting like a warmongering jerk. His goal, since his early days, was to make mankind strong enough to defend itself, keeping the truth about the Masters' troops serves to make his soldiers fight better in the defence of Earth, and his most aggressive tactics are the result of the Robotech Expeditionary Force leaving Earth to fight the war against the Masters away from there and bringing most of Earth's firepower with it (notably, the ASC scores a Pyrrhic Victory only thanks to part of the REF being sent back as reinforcements while the bigger guns are kept in the Masters' former empire by other engagements, so he was completely right about this).
Anna's parents head the Public Morals Committee and are responsible for creating the censorship laws that have strictly forbiddened pornographic material and use of crude language for the last 16 years. As a result, Japan is globally acknowledged as having the higest morality rating in the world. But their success has come at the expense of its citizens, who now lack understanding of even basic Sex-Ed. Which in turn, has contributed to Japan's already steadily declining birthrate.
Further, because Tokioka Academy has the country's highest morality rating, it's seen as irrefutable evidence that the Public Morals Act is just. Making it Anna's responsibility as its student council president to ensure that the rest of the student body continues to live up to standards. And she's fully authorized by law to stamp out all violators, swiftlyand harshly.
In Tokyo Ghoul, many Ghoul Investigators fall into this sort of thinking. While their actions might not be appreciated by the average person, they believe it to be necessary for the greater good.
Koutarou Amon begins as one, firmly believing that anything is justified in the pursuit of a better world. This includes digging around a grave site, and killing child Ghouls without remorse. After meeting Kaneki, though, he begins to question his extremist view of the world and undergoes Character Development in his quest to learn more about his Worthy Opponent.
In the Prequel, Jack, Latern turns out to be one. She's intensely jealous of the happy, peaceful lives that humans lead. Because she loves human society so much, she goes about brutally killing criminals and delinquents as punishment for disrupting society's harmony and order. This includes killing Taishi's friends, because they caused trouble at school and their motorcycles were loud and annoyed her. Taishi immediately points out the hypocrisy of this, because someone that would kill people is even worse.
Tweeny Witches: Sigma nearly manipulates Arusu and her friends into giving him the True Book of Spells and later physically brainwashes Sheila into bringing the warlocks herself as a witch they need to cast dark magic. In an attempt to get out of prison, he asks Tiana for a job to redeem himself for his failure, suggesting that the warlocks take his cellmate, Jidan, hostage to demand the True Book of Spells from the human's daughter, Arusu. However, as he reveals to Jidan, all of this is only to keep the pretense of obeying Grande. In truth, he wants to help the savior prevent the destruction of the Magical Realm so that he can avenge his father, who foretold her coming and was killed in front of him by Grande for advising against using dark magic.
Major Loki Jotunheim forces the protagonist (and many others) to become a Child Soldier and eventually declares war on Midgard. This was done so he could control all inheritors of Code Lost (such as the main character) and kill Charlotte before her Code Acht will inadvertently destroy humanity. He also orders Yuu to kill any D in danger of mating with a Dragon and transforming into the same type of Dragon, though after Volume 1, he seems more open to his subordinate's attempts to Take a Third Option.
"Black" Vritra is the one who turned girls into D, with the intent of turning them and eventually all of humanity into Dragons. Later, she reveals that she wants to turn humans into Nigh-Invulnerable Counter-Dragons to increase the chances of life on Earth surviving the next True Dragon calamity.
In Tamagotchi! Miracle Friends, Smartotchi, under the guise of X-Kamen, attempts to capture the Dreambakutchis before Miraitchi and Clulutchi get a chance to do so, thus preventing them from getting back to the future where they belong. Now, what could Smartotchi possibly be doing by collecting the Dreambakutchis? It's to prevent a piano from being destroyed in the future.
Attack on Titan has many examples depending on who's talking, but the most obvious one is Eren Yeager. He ultimately fights for freedom and peace, even if that means invading enemy nations, psychologically tormenting someone who you've already made suicidal, killing innocent civilians and making your homeland within the walls of Paradis Island a sitting target for the world's militaries to attack. Granted, from the beginning of the series he wanted to wipe out all the titans in the world, and his goal has just shifted from killing titans to killing Marleyans, but he still exhibits extremist behaviour that's similar to his enemies'.
Zeke, aka Beast Titan is similar, and can be seen as the counterpart to the above. He also fights for freedom in the form of wanting to kill off all Eldians, or, at least, stopping them from being able to reproduce.
Food Wars!: Azami Nakiri's motivation is ultimately to create a cooking world where chefs are both recognized for their talents and so that they don't succumb to the pressures brought on by being a top class chef; something he witnessed firsthand with his idol, Joichiro and his wife, Mana. However, he's done a lot of questionable and outright criminal things to achieve that end, including but not limited to ousting his own father-in-law to become Dean of Tootsuki Academy, submitting his own daughter toTraining from Hellto refine her God Tongue, and plans to shut down every single restaurant in Japan that does not conform to his standards and replace them with "true gourmet" ones.