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The Amazing Spider-Man: As part of his Sanity Slippage, Alistaire Smythe sends his killer robots out into New York City to deal with the cross-species and eventually creates a nanobot "cure" that involves destroying cross-species from the inside out, firmly convinced that what he's doing will save New York, while in reality, he and his robots are actually causing more damage to the city than the Lizard and the other cross-species ever did. He comes to his senses at the end after Spider-Man defeats him.
Dr. Eggman is another 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.
Merlina/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. This particular villain is so sympathetic that Sonic appears to have no hard feelings after it's over.
At the end, N reveals that he has been doubting himself for quite some time and battles you to test his beliefs. After losing, he leaves to find a different way to create his perfect world.
Darkrai in Pokepark 2: Wonders Beyond. He just wants Pokémon to have fun forever... which is causing the destruction of the Pokepark.
Nobunaga turns out to be this in Pokémon Conquest. He wants to conquer all of Raisen to summon Arceus, then wipe Arceus out, in order to put an end to the constant warfare plaguing the region.
Lysandre, the leader of Team Flare wants to put an end to war and "make the world beautiful". Seems like a noble enough goal... until its revealed that his method of doing so involves reactivating an ancient super-weapon to destroy all humans and Pokemon who aren't a part of Team Flare.
Omega Ruby and Alpha Sapphire, in addition to Teams Aqua and Magma mentioned above, has one in Lorekeeper Zinnia. Her goal is to summon Rayquaza in order to prevent The End of the World as We Know It in the form of a massive meteor on a collision course with the planet; her method, however, involves joining Team Magma/Aqua and helping them to unleash Primal Groudon/Kyogre in order to force Rayquaza to respond to the resultant weather crisis. When the player foils that plan, she instead starts stealing Key Stones from a large number of holders, including from the Rival (Brendan/May) and Archie/Maxie, in order to summon Rayquaza manually.
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'... In order to find the sword, he had to leave Amy behind...
Revan and Malak from the first game wanted to prepare the Republic for a war against the True Sith. Their method of doing this was to conquer the passive Republic and replace it with something stronger.
At least that was Revan's plan. While Revan maintained his goal-oriented mindset after turning to the Dark Side, Malak developed into a Blood Knight.
Except for the small fact that the Force binds all living things together, so killing it would not be a good thing!
One interpretation is that this was just a lie to force the Exile into a final confrontation, since her other stated goal is to prepare her to support Revan in the last desperate attempt to delay or stop the True Sith invasion.
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..."
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.
Tales of Symphonia: 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. He is fully aware of the irony in the fact that his plan to overturn the Score would make it a Self-Fulfilling Prophecy.
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.
Prince Kael'Thas of the [nearly wiped out] Elves is an example of this in the expansion. Kael'Thas is portrayed as an honourable man, even helping the Night Elves despite it not being a Blood Elven conflict. He simply was doing what was best for his people, even holding together the alliance with the scattered remnants of the Lordaeron humans of whom suffered a similar culling by the Scourge. Unfortunately the Lordaeron leader just so happened to be a colossal racist and it is implied he would orchestrate strategies that would lead to the remaining Elves dying off. After ordering the execution of the remaining Elves in retaliation of Kael'Thas accepting aid from the Naga (had Kael'Thas not accepted then both the Lordaeron gates would have fallen and his people would be massacured), Kael'Thas had no choice but to serve Illidan and the demon elve's agenda in order to save his people. So his choiice was either follow a path that would corrupt and ruin him, or watch his people be slaughtered for the crime of protecting their human allies.
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. 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.
One of the books explores what happens if Arthas does not become the Lich King: Jaina does. Arthas is a powerful paladin. Jaina? One of the most powerful wizards on Azeroth.
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 making 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.
Or you could not, and actually join the Master if you believe he is right and have no proof to the contrary
The Enclave in Fallout 2 want to eliminate all mutants in the wasteland and create a safe environment for the rebuilding of humanity. The problem is that their plan involves killing 99% of humanity over a slight fluctuation in DNA, not just the actual mutants, so it's not entirely on the up and up. You can, however, set the scientist behind this plan straight on morality.
Likewise, there's 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.
Both New California Republic and Caesar in Fallout: New Vegas play this role. Both crush the identities of the tribes they annex, and require its citizens to pay tribute to the ruling body (taxation for the NCR, military service for Caesar's Legion), and have been known to kill dozens to enforce compliance.
The NCR tend to be more sympathetic, as they have partially recreated modern society and promote equality among the populace, not to mention their preference of diplomacy over warfare. Yet memory of the Bitter Springs Massacre persists in the public memory, showing the extent of the Republic's wrath.
Caesar, on the other hand, merely wishes to prevent the partisanship and technological dependence that nearly wiped out humanity in the first place, even if that entails killing and enslaving thousands. His explanation is wholly rational under his strict interpretation of utilitarianism, showing he has given the matter great thought.
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.
Vayne of Final Fantasy XII subjugated nation after nation, killing their ruling royal families/existing governments, murdered his own father, and leveled a 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.
Final Fantasy loves this. In Final Fantasy XIII, the Fal'cie want to bring the world to the edge of destruction just to bring back The Maker (basically god) to recreate the world.
Although the exact reason why they want to recreate the world wasn't given and since the Fal'cie don't think very highly of humans, the reason was likely for selfish reasons so this might not be a literal case.
The Fal'cie's at least Orphan's motive is a pretty selfish one: death. They are weary of their lives of eternal servitude to a race they don't particularly like.
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.
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, ensuring peace. Lucy even says in the first game that the Templars are doing the right thing, they're just going about it the wrong way.
Of course, Lucy turns out to be a traitor to the cause at the end of Brotherhood, or at least would have been had if not for Juno's intervention, so this should have been a warning sign.
The third game reinforces the Well-Intentioned aspect of the Templars by making you play as one in the beginning. Until they are actually name-dropped it seems exactly like the Assassins.
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.
Asura's Wrath: Deus and the Seven Deities count, as everything they did was all to destroy Gohma Vlitra and rid the world of the Gohma forever, especially since Emperor Strada refused to let them prepare for future attacks during peace times. However, their plans involved killing seven trillion innocent humans and harvesting their souls to make more Mantra for power, as well as wiring Asura's daughter up to a painful-looking machine and draining her powers to enhance their own. Furthermore, most of the Seven Deities only use this plan as an excuse to gather power for themselves; only Deus and Yasha truly care about the cause, and even then, only Yasha regrets all of the death and destruction.
Chakravartin, the Bigger Bad of the game, tries to come across as this even more so. He says that he created the gohma, the very same threat the Demi-Gods are trying to defeat, to test their resolve and to see who can be his Heir as the protector of the universe, giving Demi-Gods the power of Mantra to do so. He's apparently done this quite a few times, and destroyed civilization and reset it to start the cycle again. This is even more of a subversion than the above examples, as he merely plans to do the same cycle of suffering onto other worlds or dimensions while his heir protects the universe in his place. Asura calls him out on this, merely just saying that Chakravartin is using his power for his own benefit and forcing people to do what they can't do for themselves.
The Knights of the Seal in Drakengard 2 look like this, but are ultimately either deeply messed-up people or, in Gismor's case, an outright nihilist. General Oror, on the other hand, was A Father to His Men and a genuinely good person. As for other antagonists, Caim wants to free Angelus from her suffering and Legna wants to promote his species to supremacy and obliterate the Gods — and keep in mind that the previous game established that the Gods (a.k.a. the Watchers, a.k.a. the Grotesqueries) are a pack of bastards who have already tried to destroy the world For the Evulz... and are making a second attempt throughout the finale of this game!
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 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: The Wind Waker, where 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 The Legend of Zelda: Skyward Sword, since Ganondorf is an incarnation of Demise's hatred towards the humans who defeated him (namely Link and Zelda) who will eternally pursue Link and Zelda's descendants, 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).
In The Legend of Zelda: A Link Between Worlds, we have Hilda, the princess of Lorule. She was the one who sent Yuga out to kidnap Zelda and the Sages, so that she'd be able to obtain the Triforce and restore her land, since Lorule's Triforce had been destroyed. Unfortunately, this would end up dooming Hyrule in the same way that Lorule had been doomed after losing its Triforce; but Hilda thought doing whatever it took to save her kingdom was her duty as its ruler. When Link's Lorulean counterpart, Ravio, points out that her actions are exactly what led to the destruction of Lorule's Triforce in the first place, Hilda has a Heel Realization.
This also applies to Hilda's predecessors, who destroyed Lorule's triforce because the people were constantly fighting over its power (much like Hyrule's past problems). They destroyed it to end the fighting... they just didn't know that the world would start falling apart if they did.
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.
He's also somewhat justified in the sequel, Wing Commander Prophecy; humanity encounters yet another alien threat, but this one is so alien and hostile that the only way to stop them is to either destroy or capture and blockade the wormholes they use to invade. The ending is subsequently open-ended and not in a good way, since you never learn how the aliens showed up in the first place and you never find a long-term solution to ending the conflict.
In the English translation of the Kirby Super Star game "Revenge of Meta Knight", Meta 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.
King Dedede played this role in at least one of the Kirby games where he wasn't the main bad guy. Specifically, in Kirby's Adventure (later remade as Nightmare in Dream Land), King Dedede had stolen the Star Rod from the Fountain of Dreams, broken it into seven pieces and scattered these pieces across the world, causing everyone to be unable to dream. It wasn't until Kirby defeated Dedede, and repaired the Star Rod, that it was revealed that he did this seemingly villainous action for a very good reason. It turned out that a horrifically evil entity called Nightmare had been attacking the Fountain of Dreams, thus tainting it. King Dedede made everyone unable to dream because he figured no dreams would be better than nightmares.
Fain of Lusternia was a leader and diplomat amongst the Elder Gods prior to the Elder Wars. But when the Soulless Ones attacked — wiping out all but ten of the Elder God's leaders, devouring Elders to gain their powers, and throwing the natural equilibrium of Lusternia into chaos — Fain decided to do whatever it took to defeat them. Starting with the support of his fellow Elders, he's eventually banned from his preferred method of combating the Soulless; that is, concocting an elixir of their essence to gain their powers, turning their own tactics against them. Deciding that the other Elders are weak and foolish, he forms a secret cabal of followers, concocts more of the elixir and single-handedly turns the tide of the war in the Elder Gods' favour — and in the process, he and his followers gradually becomemore and morelike their enemy. By the end of it, they're reduced to kidnapping and eating other Elder Gods for essence, and are eventually banished... completely damning the war effort. By the time of the game, Fain's the closest thing to Satan there is.
Kerghan, the main villain of Arcanum: Of Steamworks & Magick Obscura, is an example of this as 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. A more-or-less unbiased source indicates that Kerghan is 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.
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 he is.
"The very moment that Man loses his imagination, he is doomed." "It is unfortunate... but this is for the sake of protecting Earth from ... [Kali Yuga]." "I have conceived it. A method by which Man might be spared. We have chosen. This is the solution that we have devised."
In Metal Gear Solid 2: Sons of Liberty 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 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.
The Boss gave over a 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. In The Boss's case, it's more complicated than that; the nukes are bargaining chips to gain that rogue Russian military organization's trust, but nobody perceives that the leader, Volgin,has no qualms about shooting the nukes toward his homelandto satisfy his own ego. The Boss's mission is to pull Fake Defector on Volgin and to get Philosopher's Legacy to be used by the USA. Because the nukes hit USSR territory, naturally, the USA is to blame, and if The Boss wasn't killed, they might as well as started World War III. 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 overthrow 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 without them being framed for the Tanker Incident in 2007.
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.
It's a shame neither of them understood what her will truly was until the very end.
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.
Their successors were somewhat like this — they honestly believed people were dumb, panicky animals who'd kill themselves with pointless wars if they had the chance. So they manipulated a second Shadow Moses incident while attempting to launch a Big Brother Is Watching ship that would watch, control, and alter all information — to ensure peace at any cost.
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 abandoned, 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.
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.
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.
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), 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, it's 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.
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 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 against it. He then got banished out to Artania and 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'tmanage to control it. So, he became The Atoner after you re-gathered the Armaments to piece his soul back.
First is General and, by extension, Repliforce from Mega Man 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 Epsilon 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. It's the whole "evolution requires sacrifice" part that's the problem.
Then again, Mega Man 1 (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. Their reason for reactivating the four lighthouses is revealed in the second game to be to save their Doomed Hometown, Prox, and also the entire world. Although the heroes end up finishing this task anyway, Saturos and Menardi do it in the wrong way. For example, they attacked most of the soldiers and scholars at Venus Lighthouse, kidnapped several characters important to the plot, and accidentally dropped a giant boulder on Vale, "killing" Jenna's family and Isaac's dad.
The Wise One in the second game may also count. He's trying to stop the above from happening, since according to him, the release of Alchemy may save the world from immediate destruction, but it will also later lead to humans destroying it themselves. However, he also goes about it the wrong way. Toward the end of the game, he transforms Jenna's parents and Isaac's dad, all of whom were thought dead at this point, into a dragon, and he tricks Felix and co. into almost killing them.
Even 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 (immediate) consequences.
Neverwinter Nights: 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.
Ammon Jerro has an army of powerful fiends at his beck and call, murders several people who get in the way of his recovering a MacGuffin, and is canonically Neutral Evil. He's not the Big Bad, not even The Dragon. He's the former court mage of Neverwinter, trying to save Faerűn from the Big Bad by whatever means necessary. And you get to give him an absolutely epic"The Reason You Suck" Speech.
The Big Bad he's opposing, the King of Shadows, can come across as this when you meet the ghosts of people who knew him. He willingly underwent a transformation into a magical golem called The Guardian so he could protect the Illefarn empire, and everything he's done since then, from binding himself to the Shadow Weave to waging war on Neverwinter, and all the carnage he's caused, is simply him fulfilling the orders programmed into him.
In Arcanum, Kerghan is a powerful necromancer who seeks the destruction of all life... because, after centuries of using necromancy to study the place where souls go after death, he's wholeheartedly convinced that since all beings undergo suffering during life, the comparable peace associated with death is a desirable state of existence. This view is backed up by one of your party members, who is likely to have been killed and resurrected during the events of the game.
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.
Everyone but the Seraphim qualify. The UEF is ruthless and intends to use symbiotes 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 purge entire planets for not sharing their religion. Considering this, the UEF being desperate enough to use Black Sun is no surprise. The Cybran Nation are 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, Kei 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.
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.
The first game has Big Bad Kessler. His end goals are noble, hoping to prepare the protagonist Cole, his past self, for the coming of the Beast, an entity intent on destroying all life, which Kessler failed to stop in his own timeline. So by extension, he hopes to save Cole's world. He hopes to do this, however, by showing Cole firsthand the kinds of atrocities he has to prepare for when the Beast comes, as well as the agonizingly difficult choices he'll have to make for the greater good, resulting in the slaughter of thousands of innocent lives at Kessler's hands, including Cole's girlfriend and Kessler's former love, Trish
From inFamous2, we have John, aka The Beast. The world is suffering from The Plague, so John uses his new powers to activate potential conduits, saving their lives, as conduits are immune to The Plague. Unfortunately, activating a conduit consumes the lives of nearby people who are not potential conduits, with John even admitting to Cole that he wishes there was another way. In the evil ending, Cole, doubting that the RFI would cure The Plague, takes on John's role. But it's averted in this case, because Cole does it for completely selfish reasons and doesn't care about humanity. He only does it because the RFI would kill him otherwise. But hey, there's a reason it's called the evil ending, right?
Brooke Augustine of inFAMOUS: Second Son . The Final Boss reveals that she founded the DUP and began their capture and containment of all Conduits because she was convinced that it was the only way to stop the Conduits from being persecuted or killed on sight by the military. The problem is, she can't comprehend the concept of peace between humans and Conduits, and her idea of protecting them is locking them up for life and spreading vicious lies on them.
Devil Survivor has Keisuke, who, in trying to stop the public from freaking out at the Tamers, goes on a killing spree. 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 bullies' new target. Much to his dismay, the kid who he was standing up for joined in.
And in Devil Survivor 2, we have Ronaldo Kuriki, a private detective who leads a pack of rioters to attack one of the bases that belongs to the organization (JP's) that you work for. However, it's revealed that he's doing it to steal food to feed the civilians that JP's has more or less abandoned. Later when it's revealed that your boss is going to create a Social Darwinist world, Ronaldo becomes much more ruthless to stop it, even trying to kill the one member of JP's that was sympathetic toward him. However, it is possible to talk him out of this and have him become a noble human being. And it should be mentioned that the world that Ronaldo wants to create is one where people treat each other equally and work for each other's benefit. In his ending, he succeeds in doing so. It's actually pretty heartwarming.
Saren 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.
Warden Kuril, the Head of the Purgatory. Although he also uses it to gain more wealth, he clearly thinks he is doing this for the society.
Shepard can be this as well. Depending on the actions they take, Shepard 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 their crew, sacrificing a member of their crew who'd trusted Shepard to gain the loyalty of an even stronger person (Samara vs. Morinth), betraying and probably murdering multiple friends in order to gain both salarian and krogan support, etc.
Working with a terrorist organisation, routinely breaking the law, causing massive destruction of property, and allying themselves with a member of the Geth and an illegal Artificial Intelligence? Just because Paragon Shepard is benevolent, doesn't mean they won't get their hands dirty.
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 a solar system when it is destroyed, wiping out a colony of 300,000 people.
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 metalwhile still alive.
This motivation was expanded upon in the third game. The final canon motivation for the Reapers is that every organic civilization will invariably create synthethic life, which will then invariably rise up against its creators and wipe them out due to the inherent superiority of synthetics. In order to prevent the extinction of all organic life, the Reapers were created with the goal of preventing organic civilization from ever reaching that fateful war. They accomplish this by only destroying sufficiently advanced races, instead of ALL organic life. Conversion of these races into Reapers preserves their genetic code and minds, acting as a sort of testament to their existence.
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.
Omars - 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. After the inevitable wars that result, they are the only faction that is able to survive in the wastelands that was once Earth.
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.
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, fearing that they've thrown their lot in with Orlais and plan to enslave Ferelden again, and if Cailan insists on fighting with them, then it may be beneficial to remove an ineffectual king. He also feared that Cailan was about to sell Ferelden off, based on the fact that the king was a bit too eager to work with Orlesians and wholly enraptured with the Wardens, who Loghain thought to be Orlesian flunkies. In Return to Ostagar (DLC), it turns out he was right about Cailan. He was planning to divorce his current wife (Loghain's daughter) and marry the Empress, which Loghain considers the same as giving their country away.
A likely case for the Templars who care about their mage charges — the mages may be practically slaves, but the abominations of the game do show quite clearly what can happen if the mages can't control their powers and no one's nearby to quickly put them down...
Bhelen Aeducan, if crowned king, works to break down class divisions amongst the dwarves, open them up to the outside world, and start reclaiming territory from the Darkspawn again. He also declares martial law, assassinates political opponents, dissolves the Assembly, and basically drags the dwarves into the future kicking and screaming.
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.
In Awakening, the Architect's new plan is to use Grey Warden blood to create intelligent, self-aware Darkspawn, free from the call of the Old Gods... and it actually works! Unfortunately a Broodmother and some of the other newly Awakened Darkspawn decide to break away and begin an Enemy Civil War.
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 for 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.
The epilogue of Awakening mentions that should the Warden side with the Architect, this decision proved very controversial even amongst the other Grey Wardens, who are unsure whether they've just gained a powerful new ally, a powerful future new foe, or both?
Anders in Dragon Age II 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. On a more personal level, the ariefact is the same magic mirror from the first game's Dalish origin, which tainted two of her childhood friends and killed at least one of them. There's a whole lot of Survivor Guilt at work there.
EVERYONE in Dragon Age II, with a few exceptions, and once they're gone, well...
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"; "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.
This is actually averted with Meredith at the very end. She's less interested in protecting innocents than she is in finally getting a piece of the mages after so many years. Orsino, Cullen, Hawke, and Sebastian all provide alternate ways to resolve the situation with less bloodshed, including simply executing Anders, but she refuses all of them because she wants to kill the mages first and foremost.
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. 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 χ-Blade, so all his plans can never come to fruition. However, after fighting with Terra, who refused to let him harm Ven, Eraqus immediately regretted raising his Keyblade against Terra and Ven.
Valkyria Chronicles has the Atlantic Federation. Their goal is noble enough, in that they want to defeat The Empire while, at the same time, minimizing 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.
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 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...
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 2used 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.
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 games, 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. 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 villains 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.
Ra's al Ghul and his Dragon Hugo Strange in Batman: Arkham City. Their main goal was to wipe out all the criminals in Gotham by gathering them all in Arkham City and blow it all to heck!
Inquisitor Mendoza in Risen. He wants to sacrifice a whole island in order to control a powerful Titan and thus save the rest of the world.
Chairman Drek sets himself up as one, tearing off big chunks of other planets and destroying them to build a new homeworld for his people since their old world is so polluted and overpopulated that it can't support any more life. It's ultimately subverted, as during the final battle, he reveals to Ratchet and Clank that he was the one who polluted his own homeworld, and is building a new one for the money to start the process anew. Fortunately, the title duo stop him from succeeding and causing any more damage.
General Azimuth in Ratchet & Clank: A Crack In Time wants to use the Great Clock to turn back time and undo the mistake that not only provided Tachyon with the means of conquering the galaxy, but also caused most of the Lombaxes to be removed from the universe. He believes that the combined Lombax forces can better protect the galaxy, but refuses to accept that trying to use the Great Clock as a time machine could very well undo creation. Near the end of the game, he's done asking for permission. However, when he succeeds in activating the Clock and sees it begin to break down, he realizes his mistake and sacrifices himself to stop it.
Angela Cross in Going Commando, who captures and tortures Clank and collaborates with a dangerous team of mercenaries to prevent a creature known as a Proto-Pet from being released and endangering the entire galaxy.
The Faery King wants to ripristinate the visions of the afterlife the humans once had; since humans don't think about myths anymore, the Netherworld might disappear forever. However, he loses faith in humanity and tries to separate the two forever; the Netherworld would not be influenced by mankind anymore, but then the latter wouldn't be afraid of death. See below.
Livane opposes the King, and has replaced the myths of a paradisiac afterlife with the dread of death. This is because she wants humans to think about improving their lives while they can, rather than waiting for the afterlife and wrecking everything with wars in the meantime.
Also, Scarecrow. He wants to enforce humanity's fear of death, so that wars and homicides would stop.
One of the heroes in Dota 2 is known as the Anti-Mage, who, as his name suggests, seeks to end all magic in the world by killing every magic user in his path. His motivations are vengeance for the slaughtered monks of the Turstarkuri monastery, who were killed by the magic of the Dead God's Legion.
Imnity and Muriel in Duel Savior Destiny both believe they are doing the right thing. Muriel is actually an ally, so she's not exactly wrong, but she is willing to kill you if she thinks you might become the Messiah. Imnity, on the other hand, is basically the same as Rico/Oltara, but holding to a slightly different set of values that are ingrained in her very nature. She doesn't really seem to have anything in the way of malice and is every bit as concerned about her master Mia as her counterpart worries about Taiga.
In Contra: Shattered Soldier, Lance Bean is revealed to be this after he is defeated in order to expose the true Big Bads of the game, the Triumvirate. It turns out that they stole an important object the aliens have been looking for, known as the Relic of Morai, and that Bill Rizer and Lucia must destroy it.
General Morden too. He grew tired of corruption within Regular Army after his son was killed in a terrorist bombing that could have been prevented, if not for said corruption. After this, he left Regular Army and formed Rebellion Army. His goal is to remove corruption, however, the way he plans to do this is by creating a world wide military dictatorship-
Katrina in Quest for Glory IV is very much this trope. Everything she's done is because she genuinely believes it's the right thing to do. She kidnaps Tanya and takes her as her own daughter because of the draconian measures her real mother and father have taken to protect her (which border on the abusive), because clearly their treatment shows they don't really love her. She wants to release the Dark One not to destroy the world, or as a means of gaining power for conquest, but only because she fears how helpless she is during the day and thinks she is powerful enough to control Him, ushering in eternal night without the destruction and death Avoozl would ordinarily bring. Ironically, the only thing where she does not believe The End Justifies The Means is her relationship with the Hero. She wants him to help her and love her of his own free will, even though she could easily force him.
The Forerunners created the Halos which wiped out all sentient life in the galaxy, in order to eliminate the Flood. Afterwards, they then reseeded all sentient life in the galaxy, while leaving many of their artifacts for Humanity to salvage, so they can take the Mantle of Responsibility.
Albert Weskerthinks he's this in Resident Evil 5, but he's just out of his mind. (The same character doesn't even begin to qualify in his prior appearances, being The Mole in Umbrella's service in the original game and clearlylooking out for himself only in later appearances until RE 5.) Derek Simmons from Resident Evil 6 is a much straighter example, as his primary motivation for having the President zombified is to prevent the social unrest and mayhem that he believes would be the inevitable result of revealing the U.S. government's involvement in the Raccoon City incident. However, Simmons is prevented from becoming sympathetic by his lust for Ada Wong. Not only do Simmons's actions in pursuit of his lust squick out several other characters (most notably Ada herself and her Love Interest Leon Kennedy, whose disgusted reactions will most likely be shared by the player), they are also the direct cause for Carla Radames's Start of Darkness, and therefore, pretty much every bad thing that happened over the course of the game.
Nathan Dawkins becomes this in the end of Beyond: Two Souls with his true intentions revealed. The reason he needed Jodie and Aiden is to help him with his plan of using the Condenser, a device used to help spirits from the dead go the land of the living, including his wife and daughter. However, the price for this is that it caused evil poltergeists to appear and wreck havoc.
Alex Mercer in Prototype 2 is this when his actions were to end the stagnation and cruelty of humanity by releasing a virus that would turn most of humanity into mindless husks and the rest into Evolved; so similarly to Wesker, it's more self-delusion and Moral Myopia than actually having good intentions.
If Harlow in Dead Island: Riptide isn't a terrorist as Serpo claims she's this. She saves Wayne despite being infected and pushes him into the tunnels, which is filled with chemicals that are exacerbating the kuru outbreak into the zombie plague, and once he turns she goes into a Cluster F-Bomb rant justifying finding out what happens. After leading the survivors to Henderson she tries to stop you from escaping, forcibly, because there is no known cure and the infection could possibly affect the whole planet. Given the survivors of Banoi and Palanai amount to less than twenty percent without taking into account those who might be infected a Heroic Sacrifice might well have been the better alternative.
Diablo III has Zoltun Kulle, a powerful sorcerer who created the Black Soulstone to imprison demons...and angels, whom he regarded as little better. His ultimate goal was to force the angels to unlock the power of the nephalem, the powerful precursors to humans. While his methods were far too extreme (and led to him being sealed in multiple cans, he did have a few points in his favor; while he wasn't entirely right about the angels, he wasn't entirely wrong, either... and his repeated warnings about you being a pawn of someone else's plans were ones you really should have listened to.
The opponents in all three of the original Thief series qualify as this: The Trickster wants to restore nature from man's dominion; Father Karras believes Utopia Justifies The Destruction of All Organic Life; and the : Keepers want to impose their own ideal of an ordered society on the City.
Viridi from Kid Icarus: Uprising. As the Goddess of Nature, she is disgusted with the way humans fight against each other and pillage nature, so she tries to wipe them off the earth with the Reset Bomb. While Palutena and Pit agree with her views, they also say that what she does is not the solution and fight her forces to stop her Reset Bombs. Later on she joins with Palutena and Hades to fight the Aurum Invasion and when Palutena is possesed by the Chaos Kin, she helps Pit so he can rescue her.
Most of the villains in the Dark Tales series of games are outright bastards who seem to be evil purely For the Evulz. However, in the sixth game, The Fall of the House of Usher, the villain actually has a sympathetic motivation. She is the Parental Substitute of the Usher twins Roderick and Madeleine, having raised them from infancy after their mother's death. Rather than allow the Bigger Bad to kill either of them, she has therefore entered an agreement in which she acquires other human sacrifices for it, in return for it leaving the twins alone. What she does is unquestionably horrific, but you can more or less understand why she does it.
The main protagonist of the 2006 game Jaws Unleashed is a shark who eats people, destroys boats...and eliminates threats to the environment.
The Elder Scrolls V: Skyrim has Ulfric Stormcloak, who kills (arguably murders) the High King in order to lead Skyrim into seceding from the Empire- not out of any particular animosity, but because he doesn't think the Empire is willing enough to fight the Thalmor, who practically everyone agrees are pure evil.
Republic players in Star Wars: The Old Republic encounter the Justicars, a bunch of ex-military types. They return to Coruscant after the war and take over one of the sections that's suffered pretty badly and fallen into criminal control, announcing that they intend to clean the place up. The Republic is pretty thrilled by this at first... until they realize that when the Justicars say "clean the place up" they also mean "install martial law and keep the Republic itself out, violently if necessary".
In Ballpoint Universe Infinite, The Observer, master of the Logicians, turned to Lawful Evil in order to stop The Monolith, since he felt that he could not do it without being more organized and without gathering a like-minded army.