Miles Edgeworth in the Ace Attorney series. He's portrayed as an Amoral Attorney willing to do anything to get a conviction and keep his perfect record at first, but eventually, it's revealed that his use of questionable tactics are a result of genuine trust in the police's work and a massive hatred for unpunished crime, instilled in him by childhood trauma and a truly evil mentor. Though the change that comes over him is not as drastic as a HeelFace Turn, he's easily one of the most interesting characters in the series.
The murderer in the circus case from Justice for All would also fall under this trope. It's pointed out that the tragedy of this case is that nobody was really a bad person.
Case 2 of JFA may also count. The Asshole Victim had managed to shift all the blame of his clinic's manslaughter of patients to his murderer's shoes.
Godot is a shining example in the series, blaming himself and Phoenix for Mia's death, which is his main motivation for opposing Phoenix in the first place (even if he flat out admits Phoenix is not to blame). Even Maya takes the fall for the guy later in the game.
Yanni Yogi from the first game counts as this as he attacked Miles' father in a panicked state, and has to pretend he's insane, which caused his wife to commit suicide.
The murderer of the DLC case of Dual Destinies never actually murdered anyone. He did try to kill an orca, that he thought was dangerous, but he failed, and while the case's "victim" died trying to save the orca, his death was an accident, and the "murderer" actually tried to save his life. The only reason that he didn't confess to trying to save the victim after everything else was revealed was because he felt that he should have atoned with death penalty until Phoenix convinced him otherwise.
Damon Gant from Rise from the Ashes, the final case in the first game, is a prime example of this trope; he couldn't catch a spree killer and mass murderer without fabricating evidence to convict him by killing the victim of another incident and blackmailing the defendant to the Rise From the Ashes by framing her sister, Ema.
Yellow 13 from Ace Combat 04: Shattered Skies also fits this trope. Yellow 13 leads his feared Erusean squadron of aces into battle against the player's nation, and he himself is responsible for shooting down over sixty planes. Despite this, he is seen in the story as a kind and proud ace who values the lives of his wingmen more than his battle record, and who has a high degree of respect for Mobius 1 (the player character), the one enemy ace who can match him. Despite being a member of the opposing air force of the narrator and the player, he is constantly shown in a positive light, even going so far as letting the narrator and a resistance member who sabotaged his friends' aircraft escape when they were being pursued by military police.
The Strigon Team from Ace Combat 6: Fires of Liberation also fits. You can read their bios after downing their jets, and some have dialogue throughout the campaign. Most are soldiers loyal to their country, which had recently been through a brutal civil war. Their leaders, Voycheck and Pasternak, are very concerned about their squad mates' well-being, and Voycheck eventually betrays his government in order to stop their plans to destroy a predominately civilian-filled city as a way of payback, even as Pasternak sacrifices himself (and his nigh-unstoppable super-plane) to save the lives of his wingmen when he realizes that the player character would easily shoot down all of them if they all came at him at once.
Rosa Cossette DElise, the princess of Erusea from Ace Combat 7: Skies Unknown, has no personal malice against Osea, and believes that shes protecting her country from what she perceives as encroaching imperialism due to Oseas construction of the Lighthouse. However, its later revealed that she was manipulated by young Erusean Officers called the Radicals, who were looking for an excuse to use the drone army that they built using technology they got from Belka. Once she finds out the truth, and sees the chaos caused by the war first hand, Rosa defects to the Oseans to help bring about the end of the war.
General Forsythe from Advance Wars: Days of Ruin, though he declares war against the player's country in the game, barely qualifies as a villain. When Caulder offers him powerful, but horrible, weapons that could guarantee his victory in one of the early missions, he is appalled and flatly refuses. Shortly later, it is revealed that he does not kill POWs, considering it to be dishonorable. To top it all off, when he loses the war, he accepts full responsibility for the war so as to spare his soldiers and lower-ranking commanders, accepting execution by the insane, power hungry Commander Greyfield.
Even the declaration of war is ambiguous, considering that Davis is the one who says that Lazuria started it, and he probably heard this from Greyfield (paragon of honesty, that man). It's more likely that Greyfield started the war and told everyone that Forsythe did, while Forsythe hopes to end the war by defeating Greyfield. Forsythe is a Hero Antagonist.
The Controller of Armored Core 3 plays on this, as an interesting twist to the typical A.I. Is a Crapshoot. It pits corporation against corporation in pointless yet violent and often deadly battles over land or goods, is outright abusive in its control of the normal populace, and has locked humanity into underground vaults for centuries. It even, as the story progresses, seems to be going insane, making contradictory decisions and sending Nine Ball mind uploads — a character established in Armored Core to be nearly genocidal — after the protagonist and others follow its orders. It's revealed that the outside world was devastated and that the Controller was designed specifically to challenge humanity enough for them to overthrow the Controller through force and be able to defend themselves from other groups of humans.
Assassins Creed has Templars, the main antagonists of the game who murder innocent people and attempt to conquer the world. The catch? They have exactly the same goal as the protagonists — world peace — except that the Templars would rather be quick about it and use ancient mind control technology, instead of letting people decide for themselves. Another example of an Anti-Villain would be Rodrigo Borgia, who, after his defeat in Assassin's Creed II, softened up a lot and attempted to have the real big bad, his own son, assassinated to prevent him from causing further harm.
Yasha in Asura's Wrath who despite following the cause, starts to question weather the other Demi-gods way of trying to stop vlitra via Stealing human souls is the right way. Deus, to a lesser extent, is one of these as well.
Baldur's Gate: the main character him/herself, if he/she is of evil alignment (and doesn't do too many evil actions), ultimately saving Baldur's Gate in the first game and Suldanesselar in the second game.
evil joinable characters can be counted too, if they join a good aligned party, thus taking side in quests where good actions are performed, while their true motivations might be payment (Korgan), looting, exploiting the party for their personal goals or increasing power(especially Edwin) by standing aside the main character.
In Throne of Bhaal the new joinable character Sarevok could follow the main character into good deeds while still remaining evil in his heart.
In Throne of Bhaal, Balthazar, as he seeks to prevent the Five from resurrecting Bhaal and the one behind all of them from taking all the power of the god, although this implies trying to kill the main protagonist and ruling a town with an iron fist (and many merciless mercenaries).
In BioShock Andrew Ryan may or may not be one, thanks to Alternate Character Interpretation. He may have genuinely wanted to create a city free of the evils of government, but became the very evil he sought to destroy trying to protect this dream. He also forces you to kill him when you finally confront him, which may have been his one genuine act of kindness toward you. Then again, he could also just as easily been entirely self motivated. Part of the appeal of the game is not knowing.
BioShock 2 features three villains you have the option of killing. The first one is Grace Holloway, a former opera singer and a type IV anti-villain who sends various mooks after Subject Delta and calling him a monster, before it's revealed that she genuinely believes years ago he kidnapped the little girl she was caring for and turned her into a little sister, when in fact Delta was turned into a Big Daddy against his will as well.
Cornelius Slate sends dozens of soldiers to try and kill Booker, but they know Booker will win. They just want recognition for the battles they fought and to die like soldiers rather than be tortured by Comstock.
Daisy Fitzroy leads a revolution that tears the city apart, sets her mooks after Booker and Elizabeth and threatens to kill a child, but she just wants to end the racism in this city, and she was disgusted by the idea of killing a child, and only threatened to do so as part of a Batman Gambit The rest of the Vox Populi, on the other hand...
By the end of BlazBlue: Continuum Shift, both Litchi Faye-Ling and Tsubaki Yayoi become this. Litchi is forced to become a Hero Antagonist due to Arakune being captured by NOL and the only way to save him and have him cured is to get on their side, while she's still the same good-hearted woman she is. Tsubaki almost lets go of her Knight Templar tendencies and contemplates leaving NOL, until Terumi force-fed her with very harsh truths about her best friend, Noel, 'stealing her place' at the worst time possible, leaving the girl in utter despair and confusion, thus cancelling leaving NOL afterwards. She's also Jin's possible lover or Morality Pet.
From the original Borderlands1, we have General Knoxx from his own DLC, arguably the least evil of all the main antagonists in the series. He doesn't bear any sort of ill will at all towards the Vault Hunters, and is actually quite polite to them, all things considered. It's just that he has to finish his mission before he can finally leave the Crimson Lance, which is an incompetent, corrupt, nepotistic corporate private military that forces their personnel to work in truly awful environments. Because of all this, he just wants to die, and he even politely requests that Pandora ought to not exist because he genuinely thinks that people deserve better.
Though considerably more villain than anti, Borderlands 2 has Handsome Jack, leader of the Hyperion company. His goal is peace and order for the planet of Pandora, which is an honorable motive, and his Motive Rant at the end shows he genuinely thinks he's doing the right thing, repeatedly referring to himself as the hero. However, he sees kidnapping, extortion, torture, and mass-murder as a valid means for achieving that end. Also, he's kind of a dick.
Borderlands: The Pre-Sequel! both further confuses and clarifies the issue, as Jack is a bonafide Good Guy for much of the story. As the framing device is a flashback being told to characters who had already suffered Jack at his very worst, the dissonance is clearly called out. As the plot progresses, Jack gradually becomes more ruthless. His slide into villainy is evident, but it doesn't change the fact that at least some of his motivations are debatably justified.
On the flip side, the official antagonist for most of the story, Colonel Tungsteena Zarpedon, is an anti-villain in her own right. More specifically, her murdering thousands of innocents is Necessarily Evil, because it is "to save millions". In her zeal, she doesn't care who stands in her way or whether they understand her reasons.
Basically He discovers the true purpose of Ecclessia which is the ressurection of Dracula. He first sabotages Shanoa's first rite, 'causing her to turn into an emotionless wreck. He then takes the Dominus upon him, which effectively, turns him insane. Only by exposing her to the villagers and giving her the Dominus bit by bit could he show Shanoa that her mentor is actually evil. and then he dies.
Magus of Chrono Trigger is a decent enough example. In 600 A.D. he's the Fiendlord, head of an army of magical Demi Humans waging war on humanity...officially. In the meanwhile, he's brooding in his keep, trying to summon and destroy the Eldritch Abomination that took his big sister away, drove his mother to madness, and destroyed his home, while his "generals" led the campaigns and are the only ones interested in the war. That said, he did kill the heroic knight Cyrus (in self defense?) and turned Frog into a...well, frog. But hey, he has pet the cat moments.
Magus was always a slightly cold person, as evidenced by your party's encounters with his youthful counterpart, Jacky/Janus. Losing his only friends (his sister and cat), to say nothing of becoming displaced in time, simply made him moreso, hence, while he could presumably care less about whether the Guardians or Ozzie's armies won the war, he still was a wicked enough person that he probably did enjoy inflicting suffering on others (assuming Frog's flashback of Cyrus' death didn't exaggerate Magus' cruelty).
Ayla: Strange boy... But not bad boy.
In the City of Heroes expansion City of Villains, we have one of Lord Recluse's four Dragons, Scirocco. Originally a freedom fighter in the Middle East, he finds his scimitar and is granted the mantle of Scirocco, the Desert Wind. Unfortunately, as he technically stole the items, he was cursed to do only great evil, with everything he does being tainted (this might make it a subversion, as it IS a curse after all). His main motivation is to break the curse forcing him to be evil and find redemption. His actions toward heroes include mercy, fairness, and that sort of thing. When you meet him and choose him as your patron, his second story arc has you retrieve some magic artifacts for his plan to essentially rewrite the universe, turning all villains to good (or possibly killing them outright, which would probably qualify as mass murder). As a villain yourself, naturally, you end up having to stop him.
There is some debate as to whether Scirocco truly is an Anti Villain under a curse that makes him evil, or if he is just deluded into thinking he is good, but is actually only unable to recognize his evil, blaming it on other people. Given how he comes to accept who he is after his plan to change or kill all villains fails, the latter seems very likely.
In the last few issues before the game closed, Scirocco started a turn towards heroism by taking on Mot, even teaming up with Serafina, the genie who he'd stolen the Scirocco powers from. The developers stated that, had the game not closed, there was going to be an arc with Scirocco seeking redemption to become a full hero.
And back in City of Heroes, you have the Clockwork King, who started out as a nice, nerdy young man obsessed with robots who could animate piles of scrap metal using his Psychic Powers. But when those robots killed a few police officers, Blue Steelgot enraged and ended up beating him to the point where his robots put his Brain in a Jar and he kinda went a little insane. He is somewhat overprotective of Penelope Yin, a teenage girl who also has powerful Psychic Powers, and who describes him as "A nice guy who just has a problem with heroes."
N. Brio acts as this in Crash Bandicoot 2: Cortex Strikes Back. He sends much of the game's enemies (including bosses Ripper Roo, the Komodo Brothers, and Tiny Tiger) after Crash to kill him before he collects all the Crystals for Dr. Cortex, but also implores him to collect the Gems (which he uses in the True Ending to blow up the Cortex Vortex) if he truly cares about saving the world.
With the exception of King Dice and the Devil, every boss in Cuphead is one of these. While some of them can be jerks, they're all fighting in self-defense against someone trying to take their soul to pay back their debt to the Devil, and when Cuphead and Mugman defeat the Devil and destroy their Soul Contracts, freeing them from their debt, they all congregate to celebrate the duo's victory.
The second murderer in Danganronpa: Trigger Happy Havoc, Ultimate Bike Gang Leader Mondo Oowada, fits this, as while he commits a murder and had to be executed, he's the only one whose murder plan wasn't premeditated — he just snapped in a fit of rage due to stress about his hidden secret and weakness in danger of being exposed and he just saw Chihiro Fujisaki trying to overcome one's weakness instead, initiating his jealousy. After realizing that he just committed a murder, he tried to 'make amends' by protecting Chihiro's secret that he's a guy by fabricating the murder scene a bit, and when he's exposed, he shows little resistance and his only regret of dying was because he couldn't keep "The Man's Promise" he made with his dead brother. There's also the fact that throughout his time of living, while he's rather short tempered, he's pretty much a Jerk with a Heart of Gold.
Arantir from Dark Messiah was determined to keep your demon sovereign father from opening up back into the world, but to do so, he needed souls to empower the barrier. Being a necromancer with a large following, his decision was to terrorize the city of Stonehelm (a major setting) and kill the people living there. Hence near the end of the game how he said quote "A few lives for an entire world. Quite a bargain, really."
Darkstalkers has Planet Eater Pyron and Dark Messiah Jedah. Pyron was prime Big Bad material in the original games, considering that he's essentially Galactus except he destroys planets for fun, but the PS2 port of Vampire Savior showed that he recognized that there was something worthwhile in Makai and Earth and he lets them live. This wasn't the first time he spared Earth, incidentally. And Jedah, granted, has an Assimilation Plot as his grand scheme, but can you really fault him in a world where nine out of every ten demons are bloodthirsty monsters without any sense of dignity, respect, or loyalty and are just furthering their own goals? The others are perfectly nice and upstanding individuals, but they've got to worry about humans. The savior of humanity is a mentally scarred girl who is probably one step away from going Tyke-Bomb on us. A chance to start fresh and correct past mistakes can't be that bad, can it?
Samuel Hayden from DOOM (2016) straddles the line on this trope, only working with the Doom Slayer as part of an Enemy Mine situation to stop the demonic invasion on Mars and ultimately betraying him to steal the Crucible, the final source of Argent Energy. However, all his actions are done out of a genuine belief that Argent Energy, for all the risks involved in harvesting it, is the last resort for an Earth that's exhausted every other possible source of energy, and he expresses early on that he's fully willing to take responsibility for the invasion and help clean up the mess that occurred on his watch.
Ser Cullen and Ser Thrask of the Kirkwall Templars in Dragon Age II serve as the game's Anti-Villains, with Thrask seeking to aid mages on the run rather than executing them or seizing them and forcing them to join the Circle (he will, however, accept a peaceful surrender to prevent bloodshed), and Cullen turning against Knight-Commander Meredith once it becomes clear to him how crazy she has become after Anders blows up the Chantry, and Meredith calls for the Right of Annulment on the Kirkwall Circle, and on the off-chance that Hawke supports the templars, she orders for Hawke's execution instead of arrest.
On that topic, Anders himself, to some.
For that matter, the Knight-Commander herself. She saves the Player Character's life during the Qunari attack, and has no problems fighting beside an obviously-apostate mage. She seems rather reasonable until she picks up that relic and gets mind-controlled.
Knight-Commander's actions are by no means justifiable by simply being mind-controlled.. Sure, she has some excuse for her actions but later conversations specially in the next game shows that she used tranquility as punishment for crimes such as sending a love letter to a Templar and LESSER offenses YEARS before that damn idol was discovered.. At best she is a (rather misguided) well intentioned extremism.
To make it all worse, his efforts are all for nothing. Alexius tried to meddle with time magic to change his family's fate but was unable to go back far in time enough. He can't save either of them and his son is destined to die regardless of whatever Alexius does; the magister is only delaying the inevitable, even keeping his son around as a near corpse, because his death would shatter him. After the Inquisitor arrests him, Alexius is left a broken man and protests any judgement that does not result in his execution.
Speaking of BioWare, Dragon Age: Origins features Loghain, who crosses that Moral Event Horizon several times early in the game, but chiefly because he pathologically fears a re-invasion of a foreign country that had enslaved the land within most adults' memory. He didn't believe that a real Blight was occurring, just a surge of Darkspawn. When he finds out the Archdemon really is coming, he tries his best to resolve the situation. You can even have him atone by forcing him to become a Grey Warden and sacrifice his life to kill the Archdemon.
Another example would be Ser Cauthrien, Loghain's bodyguard who, despite being disturbed by her lord's actions, follows him out of duty. Luckily, it's possible to talk your way out of having to fight her. Unluckily, thanks to a bug, one of the options to do so checks against a completely unrelated skill, meaning players who use that option in their playthrough most likely still have to kill her.
Calpernia is also a good example of this trope: a former slave who wants to free other slaves and change her home country for the better, but does so by allying herself with the main villain.
Samson is a former Templar of the Chantry who was kicked out for carrying a love letter between mages (one of whom was made Tranquil as punishment) and then became burned out from lyrium addiction. He seeks to destroy the Chantry for their abuses of both Templars and mages.
DragonFable: Vayle also known as the Necromantress joined Noxus because he promised to help her revive her brother, Edgar, who Noxus killed just because he happened to be just another person in Noxus' way. She notably is not at all happy with the PC and Artix after they destroyed the spirit crystal housing Edgar's soul. Later got an upgrade into near-full hero status.
Xan is also motivated by more than simply killing stuff with fire. Understandably, he's still pissed at Warlic for being a spoiled, immature dick and trapping Jannia in a crystal.
As it turns out, Brian Westhouse in Dreamfall Chapters just believed he was protecting Stark from Chaos that unstabilises things, and just wants to go home. The fact that he was alright with the Azadi committing genocide was a mere afterthought and, in their mind, an acceptable sacrifice.
Imnity of Duel Savior Destiny is probably no more moral than her compatriots, but she's not motivated by the same things they are. Rather, she's just devoted to the White Apostle or doing her job and thus is largely lacking in malice.
King Logan in Fable III is revealed to be one. While he is directly responsible for many terrible things (such as deforestation, making Reaver in charge of industry, and abandoning Aurora) he is revealed to only be doing this to save everyone in the long run.
Lord Ishmael Ashur from The Pitt DLC of Fallout 3. Based on what you hear and learn about him as the story goes on, he seems like a textbook Evil Overlord. Then you meet him yourself, and find out that he's a more honest and fair-minded ruler than expected, who genuinely cares about his city and family, and claims to take no pleasure in his use of slaves and intends to release all of them once the mutation cure can be distributed. His alleged good intentions (he wants to revitalize the steel industry in the Pitt so as to recreate the intercontinental railroads and finally re-link the West & East Coasts of the U.S.) are compromised by the fact that Ashur's main servants are unrestrained Raiders (since they're portrayed as the only people who would willingly go into the Pitt to work for him); the squalor, pain and horror his slaves live in is utterly miserable; and he can only offer them false hope in a chance for freedom by fighting to the death, against overwhelming odds, for his servant's amusement.
Also, to some degree, Colonel Autumn. While he seems to be just as ruthless as his superior, in the last encounter, he reveals that he intends to use the water purifier to bring water to the local population, and that he did everything to prevent President Eden's planned total genocide from occurring.
President Eden himself could also count, as he genuinely believes his own PR and thinks that what he is doing is for the good of the people. He has heroic goals (restoring humanity/America and providing the whole world with food/clean water/safety) but has been misled to believe the only way to achieve this is to "purify" the world by both wiping out all strains of mutation by killing anyone mutated and enslaving the survivors for rebuilding America. He is arguable redeemable if your Speech is high enough that you can convince him he is making a huge mistake, and he will listen to you.
The best example was probably The Master from the original Fallout. He wants to forcibly turn every living human on the planet into super mutants, however, he has a very good reason. He believes that humans will just tear themselves apart fighting unless they are all one race, which you can't really argue with since you live in a nuclear wasteland precisely because humans fought, and because he believes super mutants are better at surviving, which, once again, is really solid because they are stronger than humans and are completely immune to radiation. He also holds no ill will against humans as a whole; in his new world order, humans would be allowed to live the rest of their lives safe and under the protection of his army, though he wouldn't allow them to breed. However, you can reveal to him that this plan won't work because his mutants are sterile (and not very bright), and he'll do something few other villains ever do: realize his plan won't work and just stop. That's it, not even a fight. He'll realize that everything he thought he was doing for the greater good was actually not good for anyone, and will be so stricken with grief upon realizing this that he'll kill himself and destroy the mutant army. It's sad, really, as he's probably the most sympathetic character in the entire game.
Dr. Mobius in Fallout: New Vegas DLC Old World Blues. While you're told by the Think Tanks that he's going to doom them all, the true story is that Mobius is the sanest of the scientists in Big MT, who, upon realizing that his former compatriots are all dangerous lunatics, reprogrammed their personalities into being stuck in a repetitive cycle and antagonized them with robo-scorpions to give them something to focus on, hoping that they won't try to leave and terrorize the outside world. When you finally meet him, he's actually a kindly yet a bit senile old man whose own psychotic behavior is mostly due to his addiction to Mentats and Psycho.
The Courier can be another rare playable example if you support Caesar's Legion but maintain good or neutral karma, allowing you to be a Type I, III or IV. You may be a nice guy but you're supporting a regime where all women are enslaved or subject to forced breeding (basically rape), gays, the elderly and sick are exterminated and their leader, despite shades of well intentioned extremism, has peaceful towns wiped out over personal grudges.
Mr. House can be seen as this for New Vegas. On the one hand, he wants to be the sole dictator of New Vegas and the Mojave and in his ending uses his Securitron army to enforce tight order on the territory. On the other, his reasoning is that the democracy and values of the Old World were what led to nuclear war to begin with, and his intent is to use the funds to better mankind through advancing technology, convinced that only he is capable of doing this. Depending on the player's worldview, he/she may be inclined to agree.
Dr. Noore Najjar, the vice-lord of Kyrat who runs the Shannath Arena, is a former human rights activist who Pagan Min had invited to her country, and then took her husband and sons captive to force her into selling drugs and sex slaves in order to get them freed. When she finds out from Ajay that Pagan actually had them killed years ago, which means everything she's done was All for Nothing, she decides to kill herself. That said, Noore deconstructs the premise of an anti-villain, if you read the various notes scattered throughout her territory: she tries presenting herself as more reasonable than Pagan's other Dragon, Paul "De Pleur" Harmon, by giving people drugs and booze as rewards for compliance, but she's just as much a Bad Boss to anyone who disappoints her (we see her cutting the throat of a soldier who annoyed her at the start of one mission), and Pagan thinks she might have actually started to like running the Shannath Arena. The only difference between her and Paul is that Pagan's forcing her to do his dirty work.
Yogi and Reggie, two villains who Ajay finds living in his parents' house, and who promptly drug him before sending him to Noore at the Shannath Arena. When he goes back to confront them afterwards, they desperately plead with him, saying that Pagan took away their passports when they visited Kyrat, so they're being forced to stay there and cheat rich Westerners out of their money so that Noore can extort them. From then on, they never antagonize Ajay again, except to repeatedly try out their drugs on him and send him on trippy Mind Screw visions.
Surprisingly, Pagan Min himself. Despite being the despotic king of Kyrat, Pagan is surprisingly friendly towards Ajay, treating him like a surrogate son, and disapproving of his Dragon Yuma's intent to torture Ajay's mind. Additionally, if Ajay stays at the dinner table for 10 minutes when Pagan leaves it at the start of the game, Pagan will return, thank Ajay for waiting, and take him to the place where Ajay can put his mother's ashes to rest, bloodlessly (except for that poor old man who Pagan sent off to be tortured beforehand). And ultimately, whichever of the Golden Path's co-leaders you bring to power and replace Pagan with ultimately proves to be no better than him.
Ull, the Warchief of the Udam tribe in Far Cry Primal. He's a massive, thuggish, scarred caveman who violently attacked the Player Character's tribe, the Wenja, at the start of the game, scattering them and trying to kill and eat them. We later learn, though, that the Udam are dying from a mysterious plague called "skull fire", and Ull thinks that they must kill their two rival tribes in order to ensure this. And at the end of the game, when Ull himself is dying at Takkar's hands, he begs the Beast Master to take care of his two children. Takkar, growing to respect Ull by this point, grants the Warchief's pleas.
The Shinra Corporation (or at least, key members of it, including the Turks) from the Final Fantasy VII series has elements of anti-villainy. Make no mistake, there are some outright villains in Shinra, but many of its members do have noble intentions. For instance: trying to stop Sephiroth from ending the world by launching a rocket with huge materia into space to destroy it (which the protagonists successfully disarm) and also firing the Sister Ray to kill Sephiroth (which, again, the protagonists thwart, but not before the barrier housing him is destroyed for the heroes to enter).
Yunalesca of Final Fantasy X. In life she was the first summoner to defeat Sin and give the people of Spira the Calm (the peaceful period before a new Sin is created). Now she waits in Zanarkand as an unsent to help Summoners at the end of their Pilgrimage perform the Final Summoning. She does this by turning one of the Summoner's guardians into an Aeon, the summoning of which will kill the Summoner and turn the guardian into the next Sin. Yunalesca also enforces the false teachings by Yevon that Sin will be gone forever if they atone for their past sins. And when the heroes refuse to go along with this, she tries to kill them. However she does this because she genuinely believes there is no other way to stop Sin and thinks she is preserving the hope of the people. Her last words are lamenting that the people of Spira have no hope now.
In Final Fantasy XII, most of the Judge Magisters (Drace, Gabranth, and Zargabaath) qualify, as they're simply trying to do what they consider right. Ghis and Bergan, on the other hand...There's also a case to be made for Vayne and Venat.
It's rather telling about the general tone of a story when its most depraved antagonists are dealt with earlier in the storyline, leaving the Anti Villains in charge for the final arcs...and also mention Doctor Cid.
In Final Fantasy XIII, Yaag Rosch and Cid Raines both fit this role. Rosch only attacks the party to ensure Cocoon remains protected and safe, while Raines attacks the party to stop Barthandelus' scheme.
In the prequel, Duodecim, Kuja is very similar to Golbez. Unfortunately for everyone involved, he gets Brainwashed by Kefka via application of Fake Memories near the end, ensuring his full-on villainy in the original.
Cloud in Dissidia 012 also acted as an Anti-Villain, given that he was on Chaos' side, yet also harbored some concern for the warriors on Cosmos' side. He also teams up with fellow Anti-Villain Golbez in order to fight Lightning and Warrior of Light in Prologus, and also warns them that the previous villains (Garland, the Emperor, Kefka, Ultimecia, Sephiroth, and Cloud of Darkness), as well as Golbez and Cloud himself, were actually holding back their overall power. It's also heavily implied that his main reason for his concern was because a person he knew, Tifa, was on Cosmos' side. He eventually attempts to betray and defeat Chaos so Tifa will not have to experience the same pain he has to from his experiences in the wars, and ended up being spared and recruited to Cosmos' side.
In the first Dissidia, Jecht acted as an Anti-Villain, as he only ended up fighting alongside Chaos so he could find his son Tidus and go home with him. It's later revealed that he wasn't even a Warrior of Chaos from the start, but was originally a Warrior of Cosmos. It was implied that the only reason he switched sides was because the Emperor had him brainwashed by Chaos.
Fire Emblem as a whole has the Camus archetype, which falls between this and Honour Before Reason depending on the character. While some are just suicidally loyal to a cause they don't believe in with a ruler they don't like, some of them see genuine positivity where the problem is not the cause that's being fought for, but the individual in charge. There's also cases such as the Nohr siblings (minus Xander in ''Birthright''), who abhor the villain but can't defect without significant consequences.
Fire Emblem: Thracia 776: One of the antagonists, Reinhardt, just follows orders but clearly despises the motivations behind them.
Fire Emblem: The Binding Blade: Brunnya, one of Bern's Three Dragon Generals, isn't evil at all and has serious misgivings about Zephiel's mad campaign, but cannot bring herself to turn her back on her country. This is most notably seen when she engages Roy with the remnants of Bern's army in one of the last chapters of the game. Before the battle, she gives her men ample opportunity to desert the army without punishment if they wish, since it's basically a Suicide Mission. When none of her men take her up on the offer, she forcibly sends home any and all soldiers who have children and/or elderly parents.
Fire Emblem: The Blazing Blade: the original Black Fang were heroes of the common folk for eliminating tyrannical members of their home country's government. It wasn't until Nergal showed up that they started attacking innocents.
There's also Eagler from the first 1/3 of the game, who served Lundgren because he was being blackmailed, and was truly loyal to Caelin. Kent and Sain even have fond memories of the man when Lyn asks.
They further emphasize the sympathy factor with the final boss - the Fire Dragon, where the objective is, again, not 'Defeat' but 'Kill'. Both boss fights are majorly depicted as Shoot the Dog scenarios.
Fire Emblem: Radiant Dawn has Dheginsea, who did everything he could to prevent The End of the World as We Know It and has given up and accepted judgement by the end and Sephiran, who completely lost faith in humanity after the Serenes Massacre and engineered the end of the world so that the suffering would just end already.
Both Raven King Naesala and Micaiah herself straddle the line between this and Anti-Hero, since they commit several atrocities as allies of the Begnion Empire, yet are being blackmailed into doing so by Blood Pacts which will kill all of their countrymen if they defy the Begnion senate's will.
In Conquest, they also technically count as this due to being the Villain Protagonist side. While they assist Garon and his lackeys, Iago and Hans, in the conquest of Hoshido, the playable characters do have a sense of morality and find Garon's methods questionable.
Fire Emblem Heroes strongly implies that Princess Veronica from the Emblian Empire, the Little Miss BadassBig Bad of Book I, is one of these. Xander, one of the warriors she's summoned, says she's a very sad person:
"I am also bound in another way by the deep loneliness I see in her eyes. She reminds me of one of my siblings who was once held captive in a joyless fortress. Perhaps you can understand why I could never oppose her. Or perhaps you cannot."
Fire Emblem Echoes: Shadows of Valentia introduces Berkut, a Tragic Villain. He believes that he should be the rightful ruler of all of Valentia, but as the game goes on, his continuing defeats lead him down a darker path. It is implied before his slide that he is respected by many in the kingdom and that he would in fact make a good ruler. However once Alm is revealed to be the true heir to the Rigelian throne, Berkut loses it and his penultimate acts include sacrificing his girlfriend to a Mad God and attempting to kill his cousin for being heir to the throne. After his defeat, as he is dying he lets go of his anger towards Alm and encourages him to stop Duma before it is too late.
Fire Emblem: Three Houses has the Flame Emperor, a Well-Intentioned Extremist who believes Fodlan needs to be reforged in fire, specifically by removing the Corrupt Church's leader. All of the changes he wants to implement would be for the better, and most of the main cast agrees with them on at least some level. He just wants to force those changes at sword point rather than attempt to change Fodlan through peaceful means (though it's all but stated to be impossible to do so peacefully in the Ashen Wolves DLC), and the heroes take issue with that.
It's hard to not feel sympathetic for F.E.A.R.'s Alma when one learns of her background and finds out why she's doing everything she does, and it becomes even harder in the expansion when she actively helps the Point Man by killing Replicas that are pinning him down. It's less difficult with Paxton Fettel, who starts off as a cannibalizing monster who has no problem killing civilians for getting in the way, and, later on, tries to kill the Point Man out of anger that the Point Man killed him.
Fettel's case becomes a bit more understandable when you consider the fact that his grandfather deliberately made him that way.
The Frog Prince, in the second Dark Parables game, falls into this category. He's been causing disappearances in the Black Forest of Germany, and threatens the player character more than once...until it's revealed that he's immortal, and wants desperately to die and be reunited with his deceased wife.
In Sins of the Fathers, we have Malia Gedde, who was pretty much forced to become the high priestess of a murderous Voodoo cabal and suffered the voodoo equivalent of Demonic Possession to boot. And even so, most of her villainy was of the Pay Evil unto Evil variety, and none of her deeds were merely For the Evulz. (Even trying to kill Gabriel and Grace could be justified by their trespassing.)
In The Beast Within, we have Friedrich von Glower, the Black Wolf, who inherited the werewolf curse from his father when he was twelve, through no fault of his own. While he has gotten blood on his hands since then, he hasn't personally killed anybody in decades and seems genuinely convinced that the werewolf curse can be controlled. (Of course, his beta werewolf, Von Zell, is much less sympathetic.)
Saturos and Menardi in Golden Sun and Agatio and Karst in Golden Sun: The Lost Age are interesting examples. In the first game, they appear completely ruthless and apparently want to light the 4 lighthouses to abuse the power of alchemy. After their defeat at the hand of the player, Felix, who was believed to be merely held captive by them, tries to continue their goal. In the second game, it is revealed that the "bad guys" were actually trying to save their homeland (and, by extension, the world) from destruction and were merely justifying the means. The heroes of the first game later join Felix's group in their quest to activate the lighthouses and actually work together with the replacement new "villain" couple.
One reason it's an interesting example is the fact that the first game only gives you information that Isaac, Garet, Ivan, and Mia know. When Saturos is fought on the top of Mercury Lighthouse, Jenna seems to try and warn them... not of the fact that Saturos is right there behind the beacon, but that they are actually doing what is good for the world. When they are fought at Venus Lighthouse? Jenna and Kraden aren't there at all.
Anji Mito of Guilty Gear happens to be one of the last living Japanese, so he's out to find a way to live forever. In one of his endings in XX, That Man approaches him and offers him a way to be young and immortal in exchange for his servitude, and Anji actually says yes, which is why he works for That Man in Accent Core +. Despite this, Anji doesn't fully trust That Man, and remains a cheerful, friendly (as in genuinely nice friendly, not the other kind) guy.
That Man himself, whenever he appears, isn't that bad of a guy either, despite being a mysterious schemer. In fact, Xrd reveals that he's been working to stop the schemes of a much more dangerous villain. His greatest sins are creating Justice (who eventually decided to hijack control of her fellow Gears to try and Kill All Humans) and employing the wildly unpredictable I-No, with her bad habit of screwing with the protagonists For the Evulz.
Half-Life 2 has Dr. Breen. He surrendered Earth to the Combine, and is now their administrator on Earth. Breen has presided over an Orwellian regime that has (among other crimes) prevented humans from reproducing, raped and despoiled the environment, turned dissenters into mindless servitors, and used biological warfare on a regular basis. However, Breen himself is a rather affable character. He seems to honestly believe his own propaganda that the Combine is offering humanity a chance to evolve into something new. He refers to the rebel leaders (most of whom are former employees of him) as "old friends" and, rather than using force to put down the uprising, tries to get the rebel leaders to surrender. However, killing Eli Vance would be unforgivable.
Some of the creator commentaries and conceptual artwork for Half-Life 2 suggest that Breen's Deal with the Devil really did save humanity, even if it reduced the survivors to slaves.
However, Breen is also an arrogant puke whose mask of affability slips considerably as you get closer to his inner sanctum. By the time he's rising to the teleporter at the top of the Citadel, you're really, really ready to crush his guts for good. And his threats to the Overwatch during the assault on Nova Prospekt. He's just a really well-adjusted, banal, completely evil dude.
Mustache Girl from A Hat in Time once lived a normal, happy life until the Mafia Goons invaded her hometown and took it over. By the time Hat Kid encounters her, she has become a snarky, rebellious individual who is willing to go to any lengths possible to throw them out of her hometown. Upon discovering the power of the Time Pieces, she reaches a Hope Spot but is quickly let down by Hat Kid's refusal to mess with time (Hat Kid is also an Anti-Hero who shows little interest in helping others unless it means recovering her Time Pieces). This results in a Villainous Breakdown and the end of their friendship, culminating in a robbery of Hat Kid's Time Pieces and the creation of an Alternate Timeline where she rules as Judge, Jury, and Executioner over all other characters encountered in the game. Unstable as she is, it's hard to not feel some sympathy towards her for what the Mafia did to her hometown.
And, in the ending where only he and Ethan survive, he is so impressed with Ethan's tenacity that he offers to let Ethan kill him, having finally seen a father willing to sacrifice everything for his son.
While this trope is debatable in the case of Jacket, Hotline Miami gives us Richter, the masked assassin who murders the girl Jacket saved and put Jacket into a coma in an attempt of killing him. His first (true) appearance is relaxing on Jacket's couch one night after a mission with a gun in hand, tries to give him a friendly greeting, before insisting on getting it over with and fires a round into Jacket's skull. When Jacket goes on a Roaring Rampage of Revenge to find Richter, the rat-masked hitman asks if Jacket had been getting those phone calls as well, and insists that he was Just Following Orders before awaiting Jacket to kill him (the player is allowed to walk away without killing him at this point.) ''Hotline Miami 2: Wrong Number reveals that not only Jacket spared Richter's life, but Richter was caring for his deathly ill mother, and only goes through with the 50 Blessings plan when they torch his car and threatens his mother's life.
Lord Ravannavar is a borderline example as while he is a ruthless Omnicidal Maniac, its only because he seems to honestly believe the world has reached its natural end and that it (and all the people he kills) will be recreated in a superior form once Kala is awakened... and he's arguably right, given that the world has been destroyed and reborn many times over, and this iteration would have been as well if not for the Four Heroes disrupting the cycle by sealing Kala away years ago. He's just unaware that Kala's cycle is her desperately making and unmaking the mortal realm to try and make a perfect world through Save Scumming rather than any sort of natural divine process.
A rare PLAYABLE example is Cole, protagonist of inFAMOUS, at least in inFAMOUS 2. The evil options in inFAMOUS 2 tend to be immorally pragmatic while the evil options in the first inFAMOUS tend to lean towards Kick the Dog at times, especially if you activate the second ray sphere, killing a lot of people to boost your powers.
Surprisingly, main antagonist Kessler. Him doing all the evil things was actually his intention to prevent the grim future and ensure Cole would destroy it.
And another shock, the Beast himself, who, it turns out, is killing with the intent of awakening the dormant powers of Conduits and sparing them from the plague so at least SOME people will live. He REALLY doesn't want to do it, but honestly doesn't see another way.
Axel of Kingdom Hearts fame. Even though Yen Sid says that the Nobodies don't have hearts and are thus incapable of any genuine emotion, it's difficult to think of his motives as anything but sympathetic, not least thanks to his de facto HeelFace Turn leading to a Heroic Sacrifice in the end.
He's pretty much a hero at this point, even to the point of being a keyblade wielder and telling Sora and Riku that he'll be a master soon enough.
To some extent, nearly all the members of Organization XIII fall under this trope, particularly in the fandom. Although most would agree that Xemnas was always a megalomaniacal psycho who was manipulating the others' strong desire to reclaim their own hearts, even Saix displayed such pitiable qualities by the end.
Recently revealed is that at least Xigbar is just as bad as Xemnas. With him working for Xehanort for a long time and him being "half Xehanort" for likely for just as long, Xigbar has no redeemable qualities. Who knows if Saix is just as bad.
Oh, and the reveal that Nobodies can regain new Hearts over time if they go through an especially emotional experience. This practically makes every member of Organization XIII oblivious to the Organization's connection to Xehanort an Unwitting Pawn.
Riku, to a certain extent, at the beginning of Kingdom Hearts. Even when he is 'seduced' by Maleficent and starts being a thorn in Sora's side, it's only so that he can rescue Kairi.
Dedede's Anti Villain status is even included in the story mode for Super Smash Bros. Brawl where he starts stealing the trophies (corpses) of various heroes from Wario, presumably because he's trying to complete the same evil task as the other villains. He takes them to his castle and puts strange Dedede pins on them. Turns out, these pins are time-release detrophyfiers that bring said heroes back to life just in time for them to become the final resistance against the real villain. Dedede even selflessly gives his own pin to whichever princess he captured when he realizes that he doesn't have enough to save himself and the heroes.
You set Revan's alignment at the being of the game, so it doesn't matter how evil or good you played him, only what you choose in the beginning of II. Revan is portrayed as someone with motivations so strong that he freely moves back and forth from Sith to Jedi as his plans demand without getting fixed on one view, which was part of KotOR II's whole deconstruction of Star Wars and the Force.
Some hints are dropped that the outside threat is the Yuuzhan Vong. Because the game postdated the New Jedi order books, this was intentional.
Although some suspect the huge Empire in the unexplored regions run by the original Sith might have something to do with it.
With the upcoming MMORPG, it's confirmed that the threat was the 'True Sith' spoken of by Kreia near the end.
Though he has crossed over through antihero and into full blown hero by the end of the series, Kain of The Legacy of Kain fame fits the bill during Soul Reaver and Blood Omen 2. He crosses into antihero-dom somewhere during Soul Reaver 2.
Though he believes himself to be The Hero, it turns out that Raziel, by virtue of being an Unwitting Pawn, is actually an anti-villain.
The Legend of Zelda: The Wind Waker: This game's Ganondorf spares the lives of prisoners he has no need for, even going so far as to subdue, rather than kill, Link himself (at least until his goal is destroyed and he completely snaps for the final battle). He also explains his original motive for wanting to take over the world: The harsh desert winds brought death, suffering, and ruin to his people, but in other, greener regions, it meant something very different.
Ganondorf: I coveted that wind, I suppose.
The Magic Emperor from Lunar is a definite example. He plays a Card-Carrying Villain for most of the game, but his motives are not entirely selfish. He decides to take over the world because the Goddess Althena abdicated her role and left humanity to fend for itself. His true desire is to save humanity from itself, as is made obvious by his clear anguish during his FaceHeel Turn. He also pulls a HeelFace Turn in the sequel.
Durandal from Marathon could be this, depending on how one interprets him. He's a self-aware AI that was meant for operating doors and elevators on a colony ship, and he ended up bringing a lone ship from an alien race of slavers to the ship. He does this all as a part of a big gambit to become God of the next universe. Despite his seemingly selfish goals, he does allow the humans that the Pfhor enslaved (which he used as his army) to return to earth on a captured Pfhor vessel. And he may honestly believe that he is humanity's only hope, as he does go out of his way to keep the Pfhor from finding Earth.
Matriarch Benezia is another example of this. The reason she joined Saren was to persuade him away from the dark path he was walking. Instead, she got her free will destroyed via indoctrination by Sovereign.
David Archer in the DLC Overlord in Mass Effect 2, whose brother tries to upload his brain into a VI to control the geth. Instead, it drove him insane and resulted in one of the most heartbreaking moments in the game.
Aria T'Loak, bitch-queen of Omega. She professes no virtues beyond self-interest, and permits all manner of crime but she does try to keep some semblance of order, such as enforcing a quarantine when a plague breaks out. In Mass Effect 3, she recognizes the Reaper threat, and puts her own personal vendetta against the Illusive Man on hold to help you defeat the Reapers, uniting the various mercenary companies to back your cause — under her command.
The Illusive Man seeks to protect humanity's interests in the galaxy, whatever it takes to do so. He has Shepard brought back from the dead in the second game so that they can stop the Collectors from abducting humans. The Illusive Man also seeks to stop the Reapers, but ultimately becomes indoctrinated trying to find a way to control them. In his final moments, he either expresses how he tried to fight the Reapers before shooting himself or tells Shepard how everything he did was for Earth after he is fatally shot by Shepard.
The Catalyst was created in response to organic races being wiped out by the synthetics they had created, tasked to preserve organic life. It decided that the best choice was to create the Reapers to regularly harvest all organic life and convert them into nigh-immortal Reaper form. The Catalyst helps Shepard to reach it and, admitting the Reapers to be a flawed solution, allows Shepard to decide upon a new "solution".
In the ever-changingMega Man X backstory, some of the mavericks only joined Sigma's rebellion out of loyalty (though others joined because of The Virus or willingly out of less noble reasons). Particularly sad is Storm Eagle, who, depending on the continuity, fought against Sigma before being defeated, and either joined him out of some sense of duty or due to being forcibly converted by the virus (retaining enough of his old personality to be reluctant to do what he does), or (in the manga) was actually a double agent working for the Maverick Hunters but didn't drop the act until after X did irreparable damage to him.
Similarly, Repliforce from Mega Man X4 started out as a paramilitary organization fighting alongside the Maverick Hunters, but after a combination of their failure to stop a surge of Maverick activity leading to suspicions that they themselves are Maverick, a visit from Sigma to sow paranoia that their human masters will eventually dispose of them when they stop being useful, and being suspected of being responsible for the destruction of Sky Lagoon, they decide to break away and form their own independent nation only for Reploids, becoming the first political Mavericks.
The Guardians of Neo Arcadia in Mega Man Zero (especially Harpuia) are even more sympathetic. They see it as their duty to protect Neo Arcadia and humankind at any cost, and eventually develop a friendly rivalry with Zero. Once Big Bad Weil takes over with a corrupted version of Copy-X, their loyalty to Neo Arcadia is strained to its breaking point and they finally side with Zero to fight against Weil.
Also, Craft, who was only a villain for two reasons. The first, because Weil controlled Neo Arcadia and could kill anyone he wanted with that power over the Reploids and humans. The second, so that Craft could rescue and protect Neige before Area Zero was destroyed. It ended up making him go Maverick and fire Ragnarok's laser cannon RIGHT AT WEIL.
Big Boss in Metal Gear 2 probably qualifies as one. When fighting Kyle Schneider, he reveals that Big Boss was the one who saved his resistance from the Outer Heaven bombings commenced by NATO (in case you're wondering why this is notable, it's because Schneider was opposing Big Boss's group, Outer Heaven). His men all follow him, not out of any fear or brainwashing, but because they genuinely love him, as he cares about all of them.
Not just him, but his mentor, The Boss from Metal Gear Solid 3, counts as well. She was branded as a traitor of America even though she was actually a Fake Defector who was just trying to defend her country from the inside of Russia and would bear the World's hate on her shoulders to do so. It's her death by the hands of Big Boss himself that turns him into an Anti-Villain in the first place.
Solidus Snake created a terrorist group to oppose the Patriots, but he only intended to do so because the Patriots were trying to eliminate everything America stood for (Liberty, for one thing), and he also took in people no one else wanted (eg, Ocelot and Olga, who ironically [and unfortuately for him] turned out to be Patriot agents, although the latter was an unwilling agent), and not out of any desire for power. It's also hinted before the mass RAY battle that although he intended to kill Raiden, he was saddened to have to do so, especially when the Patriots essentially brainwashed Raiden.
Senator Armstrong of Metal Gear Rising: Revengeance wants to destroy the US government... But he argues, is that really such a bad thing? He argues with the established system gone, there'll be no more weak, corrupt politicians playing people along. Armstrong wants to create a new, powerful America where every man and woman is free. This may come across as a case of social darwinism, and he isn't above starting wars or using Child Soldiers to meet this end, but he's notably the only Metal Gear who doesn't want to use nukes and genuinely respects Raiden and wants him to join his side. In the end, he's just fighting for what he believes is right for his country. Even the lyrics for his theme song compound this:
Reptile from Mortal Kombat is typically portrayed in a somewhat sympathetic light; while most of the villains are after absolute power, he is always attempting to resurrect his race, of which he is typically portrayed as the sole survivor. He is, however, still completely willing to kill for his masters in order to see this through. In most of his endings, Reptile is betrayed by his far more evil masters, and his goals are never realized.
Saavedro from Myst III: Exile. Spending twenty years trapped in four uninhabited worlds while his people, including his wife and children, were stuck in dying world waiting for help that would never come didn't do much for his sanity. By comparison, he's much less evil than the antagonists in previous games, of which, Sirrus and Achenar were the very ones responsible for stranding him and dooming his world. His reason for wanting revenge against Atrus is due to holding him responsible for his two sons becoming monsters and his antagonism towards the player is merely because they're an ally of Atrus and accidentally got stuck in Saavedro's trap instead.
Due to the way the Nasuverse treats antagonists, you can end up as enemies of people who may be really, really evil or crazy; they, at least, have good kills. For example, Arcueid and Akiha are both love interests, and they can also go rather yandere over Shiki. Ilya is a confused girl who can't decide if she hates Shirou for being Kiritsugu's (apparent) favorite or likes him because she's his sister, or Lancer, who serves Kotomine out of his personal sense of honor and, because Kotomine has none, turns on him in both Fate and UBW. Even Kotomine gets an A for Effort in Fate/Zero and Heavens Feel route despite numerous rather unpleasant to downright sadistic things he does For the Evulz. Also, Walachia/Tatari is a horrible, horrible monster because...he's trying to avert the doom of mankind, which can't be done, but as far as he knows, turning himself into what he is now is his only shot. Motive Decay is sort of inevitable when you stop being an actual entity though.
the Big Bad himself can come across as this, when you visit the Illefarn ruins and meet the ghosts of people who knew him before he became the King of Shadows. Everything he's done, from utilizing the Shadow Weave as a power source when the original weave died, to waging war on Neverwinter, and all the carnage he's caused, is simply him trying to fulfill the purpose for which he was created, preserving the Illefarn empire.
Mask of the Betrayer has The Founder. She inflicted the player character with a terrible curse, and set in motion a chain of events that threatened the very fabric of the multiverse, all to save her lover from a fate more horrible than death. It is hard to consider her a villain, despite everything.
Zero, the mastermind behind the Nonary Game in Nine Hours, Nine Persons, Nine Doors. The primary reason for the current Nonary Game is to produce a Stable Time Loop to ensure that she doesn't vanish in a Temporal Paradox (she was forced into the previous Nonary Game 9 years ago, and only survived because she psychically linked with Junpei in the present day, who helped her solve a puzzle that would've gotten her killed if she hadn't.) To that end, a good deal of claims about the lethality of the current Nonary Game are made up (the group isn't in a slowly sinking ship, but in an elaborate underground facility in the Nevada desert, and other than the people who organized the previous Nonary Game, nobody is actually armed with a bomb that will kill them if they break the rules.) In the Golden Ending (which is what Zero is aiming for,) the only people who die are the previous organizers, and even then Ace is left alive to pay for his crimes after he's forced to admit them.
Commander Vladimir from No More Heroes 2: Desperate Struggle doesn't even realize that he's in a deathmatch with Travis when the two fight. He's just returned to Earth after twenty years in outer space and has no idea about the fall of the Soviet Union. Throughout the battle, he frantically tries to contact his defunct mothership, defending himself as best he can from Travis using his Kill Sat. By the end of the battle, when Vladimir finally catches on, even Travis feels sorry for him.
Ingway from Odin Sphere fits this trope perfectly. He does too many bad things to list (mostly for the sake of gaining power or furthering his plans of revenge), but it's hard not to feel bad for him once you realize that he's still tormented by guilt over "abandoning" his mom when he was a child and making Velvet his scapegoat for their grandfather's wrath, and he only activated the Cauldron and destroyed his country in hopes of protecting his father's army from certain annihilation by his grandfather's much stronger one. He shows immeasurable kindness to Mercedes (his last words are about how he hopes she's safe and he wishes he could see her again), distracts Urzur by fighting him while he lets Cornelius (whom he loathes and tried to eliminate partly to keep him away from Velvet) go on ahead to save Velvet, and when Armageddon begins he attempts to avert it by fighting the Cauldron as the Beast of Darkova.
The titular Evil Overlords of the Overlord games occasionally fit into this category because they are usually fighting people just as, if not more, evil than they are. The first game gives you the opportunity to play a Noble Demon who's taking down Fallen Heroes that have devastated the land. Overlord II has you playing as his son, who, despite being even more potentially evil (there is no Noble Demon option), is still taking on the genocidal Glorious Empire that's attempting to destroy all Magic, and the endgame involves you destroying the all-consuming Eldritch Abomination that the Emperor has fused with in his bid for Godhood.
Symmetra is by default a good hearted lady... except she's pretty much the top enforcer of VishkarCorporation, a very Knight Templar organization that have no qualms about making people suffer in order to describe their brand of order while getting more profits. Symmetra is baffled with their underhanded methods, but believed that maybe they're doing it For The Greater Good... which was because she was kidnapped from her old life of poverty by themselves and quite possibly indoctrinated with their philosophies from young age just because they want her talent in Hard Light manipulation. Word of God states this was intentional — she is described as not being a villain in the sense of Reaper or Widowmaker, but people in-universe may view her as a villain.
Doomfist also fits this trope. His beliefs align with social darwinism, and despite being a leader of the terrorist organization Talon, his ultimate goal is to make humanity stronger. In order to achieve this, he plans on plunging the world into another great conflict through Talon. Overwatch is all that stands in his way.
Very few of the villains in the Parascientific Escape series are truly evil. Misaki was manipulated into committing a crime they regretted, Tsukiko grew up in such horrible conditions they have serious trauma, and Ritsu, though the closest to "evil," was also manipulated by the more Chaotic Neutral Iori.
Conversed about in Persona 3 Portable. Junpei doesn't like anti-villains, because they're not as satisfying to beat. If you played the original PS2 game beforehand and already know about his relationship with Chidori and friendship with Ryoji, you'll understand the irony.
In Persona 2: Eternal Punishment, Kandori Takahisa has learned Being Evil Sucks, and just wants to settle the score with his old enemy Kei Nanjo.
In a rare instance with PersonaBig Bads, the Big Bad of Persona Q: Shadow of the Labyrinth, the Clockwork God isn't evil at all; He's just trying to depart Rei to the afterlife just like the party and Zen, but only in a merciless fashion. The only reason why you need to fight him is to make Rei rest in peace.
Another example is the True Final Boss of Persona 5Royal. You might expect that they are some villain that is more vile and sinister than Yaldabaoth, the absolute worst that Persona can offer, but you are wrong. The true final boss is none other than one of your confidants Takuto Maruki, who was trying to make his very own utopia with no suffering or pain using the power of Mementos, effectively making a scenario that isn't very short of being The Fall save for the bodies are still there and living. Even then he didn't do it on his own accord; He's heavily implied to be an extra consequence of Yaldabaoth's plans because Yaldabaoth somehow managed to unintentionally corrupt his Persona and he was driven berserk alongside it.
Pokémon Mystery Dungeon: Explorers has Grovyle, which has been built up as the villain for the game's first half for stealing the time gears. In reality, that was a lie made by Dusknoir and the gears are taken by him to stop time from stopping.
Pokémon Black and White has N, who's a particularly heartbreaking example. All he wanted to do throughout the entire game was to liberate Pokemon from trainers, who he believed were abusing and enslaving them. And then you find out that the entire team he was meant to be in control of was just a front for Ghetsis to trick the world's trainers into releasing their Pokemon so he'd have no opposition, and he manipulated N into spreading this word and asserting himself as a hero so Reshiram/Zekrom would appear before him and Ghetsis could indirectly (or directly) have control over them as well. And that he deliberately raised N to fulfill this role, segregating him from people and letting him be raised by Pokemon who had been abused by trainers, so he'd believe that Humans Are the Real Monsters and that this was the inevitable result of Pokemon/Human interaction. When N finds this out, he's noticeably silent...at which point Ghetsis laughs, calling him heartless and a warped boy who understands nothing but Pokemon. Once that's over, though, he immediately agrees that the PC is right. The game even lampshades his Hero Antagonist status - when he expresses understandable distress over the reveal, the other characters point out that the legendary Pokemon Reshiram/Zekrom did recognize him as a hero and allow themselves to be captured by him. He didn't know the truth, but he was still the hero of ideals.
In Pokémon X and Y we have AZ. Formerly the ancient king of Kalos from 3000 years ago, his Floette, one he loved very much, ended up in the great war, and died, being brought to AZ in a small coffin. This saddened, yet angered AZ, creating a machine that would revive his Floette. He succeeded, but his pain and anger was too great, as he converted his machine into an ultimate weapon that ended the war in one fell swoop. Yet after all this, his Floette, shocked and saddened at his action, left him, as he killed many Pokémon to power his machine. The resulting energy left him and Floette immortal, reducing him to Walking the Earth, trying to atone for his sins. He succeeds in the end, finally letting go of his anger and meeting his Floette after 3000 years of searching.
Pokémon Ultra Sun and Ultra Moon proves how separate they are from Pokémon Sun and Moon by telling a much different story of the Alolan Island Challenge, proving how"This isn't the Alola region you thought you knew...." Most Pokémon villains seek to use Pokémon for their own evil, wicked, cruel, and twisted purposes, but when you face the Aether Foundation President Lusamine, you'll see how different she is compared to Pokémon Sun and Moon, and find out that she's a perfect example of an Anti-Villain this time, and a much likeable one as well, even more than N from Pokémon Black and White, with most of her dialogue being much nicer and her motives being more altruistic. For the most part, Lusamine's plans to use Cosmog's power to open the Ultra Wormhole are still the same, which is still a major plot point in the story, but this time, it's for a different purpose; she doesn't care about the Ultra Beasts and letting them run wild in Alola this time. Instead, she's trying to go into the Ultra Wormhole and stop Necrozma from stealing Alola's light the same way it did to Ultra Megalopolis. For this reason, she recruited the Ultra Recon Squad, four extraterrestrial people from Ultra Megalopolis, to assist her, as they also wish to stop Necrozma through any means necessary. All the while, Lusamine isn't as abusive to her children as she was in Pokémon Sun and Moon, as she only berates them because she felt genuinely betrayed by her own children. When she disowns Lillie for leaving her and stealing Cosmog, she's visibly upset, but not enraged; She genuinely feels hurt and betrayed that, Lillie and Gladion, her own children, took Cosmog and Type: Null, respectively, away from her, then ended up leaving her 3 months.
The Big Bad of Pokémon Sword and Shield is Rose, Chairman of Macro Cosmos. Why does this character turn to villainy and summon Eternatus to bring about the Darkest Day? To solve a looming energy crisis, one that is over a millenium away at that. The only reason he even qualifies as an antagonist is that he's too impatient to wait a single day and ensure that Leon isn't too busy fighting you for the Championship to help him contain Eternatus. Prevention may be the best cure, but his impatience made the cure worse than the problem.
In Prince of Persia (2008), the Warrior might count. He was the king of a pacifistic people besieged by enemies, and sold his soul to the dark god Ahriman to fight them off. Ahriman turned him into an invincible hulking monstrosity; the Warrior destroyed these enemies and then left to serve Ahriman, knowing he had become something anathema to all that they were. Of the four Corrupted the Prince and Elika face, he's the one saying he doesn't want to kill them, they should run, no one can win against a god. Elika thinks his last act before dying in a burst of light, hurling her and the Prince away, was Redemption Equals Death. The Prince doesn't share her opinion.
The Prince himself may count. He spends the entirety of the game as the Hero until the very end of the game, where he places his own wishes/emotions not only ahead of the safety of the world, but the wishes of Elika herself, by undoing all he did throughout the game in order to resurrect her, releasing all the evil back into the world.
Katrina, of Quest for Glory IV. She sees herself as the benevolent ruler of Mordavia and to her credit actually does try to do so. She arguably saved Boris's life by hiring him as gatekeeper (and notably did not turn him, or apparently even try to stop the Hero from reconciling him with his wife), and she genuinely believed she was doing the right thing by taking and turning Tanya, feeling that the girl's parents were cruel and didn't really love her. Many of her actions (such as her attempts to seduce and manipulate the Hero) were also driven by her own deep loneliness and desire to be loved. Finally, the only reason she sought to release the Dark One was out of fear that some day, someone might slip into the castle and stake her while she's lying helpless in her coffin during the day. She thought she could control the entity and bring on eternal night, and had no desire to destroy or conquer the world; she was content ruling Mordavia. And she genuinely fell in love with the Hero, ultimately leading to her Heroic Sacrifice, and eventual HeelFace Turn if the Hero resurrects her in Quest for Glory V.
To an extent, Baba Yaga in Quest for Glory I. She's certainly an evil, cannibalistic witch with a Hair-Trigger Temper, but all she really wanted was the be left alone. In fact she only cursed the Baron and his family when the Baron attempted to drive her out Spielberg Valley, and doesn't do anything to interfere with the Hero. She also gets along well enough with Erasmus (although she cheats at cards), and by the time she appears again in Shadows of Darkness, she's completely willing to overlook the events of the first game, and aid the Hero on a number of minor and major quests (though it helps he brings her something other than himself for her to snack on...)
Certain characters in Saya no Uta. Yeah, Fuminori has crossed the Moral Event Horizon at some point, and continues to Kick the Dog by regarding Yoh as his sex slave after Saya mutates him. Still, you gotta pity him when he loses his beloved Saya, the one person who comforted him. His condition he's had from before the story started. Can't really blame him for hating everyone other than Saya. Saya, for her part, just wanted to find love, but it is in her nature to die and mutate the planet's entire population, and she also meant it as a gift for him to make his life still worth living after her's ended. Meanwhile, Kouji and Dr. Tanbo are out to kill the two of them, but only to avenge Yoh and to save humanity, respectively. And let's also mention Yousuke, who only killed his wife and daughter, and then tried to rape Saya because of psychosis after Saya corrupted his brain earlier on.
Shadow Hearts' Albert Simon may be trying to end all life on earth, but he's doing it because he's fed up with the fundamental injustice of human society.
Shadow Hearts: Covenant: Kato was a mild-mannered, devoted NPC on the heroes' side in the first game, who lost the woman he loved. This leads to him becoming a major character in Covenant. Though he works as part of the Japanese conspiracy which puts him in an antagonistic role to the heroes, he sympathizes with Yuri's loss and offers encouragement and support where he can. He only shifts completely into the role of main antagonist after he loses his lover for a second time, and then, he offers the Emigre Manuscript to Yuri so he can attempt to resurrect Alice.
Wander, the main character of Shadow of the Colossus, fits in well with this trope throughout the entire game. While his motives are pure (he wishes to bring his lover back to life), in order to achieve them, he makes a pact with a dark god (and the dark god warns him of the consequences of his actions and tries to dissuade him from his course) that involves going out into the world and slaying sixteen creatures (the colossi) who, up until his arrival, had lived in peace.
Also the Dark God Dormin Themself. Not only do They try and discourage the protagonist from resurrecting Them, at the end of the game despite being either killed or resealed They still honour the bargain and bring the woman back to life.
Also, from Silent Hill 2, we have James Sunderland, murderer and all around sympathetic guy.
The Kurvasz Special Ops from Solatorobo. In addition to being able to find pictures of them goofing off, they believe they're just following orders, though Opéra later admits she questioned Bruno's sanity as time went on and was mostly loyal to him based on how he had been years before. After you defeat Bruno, they even do a HeelFace Turn and begin helping Red, turning their methods for controlling Lares into a method for permanently stopping it. Béluga counts as well, as he was only working with the Kurvasz to try to spare Elh the pain of having to do the Rite of Forfeit to seal Lares again.
Shadow started off as one in his debut appearance in Sonic Adventure 2. His goal was to use the Chaos Emeralds to destroy the world with the Space Colony ARK crashing down towards it in order to avenge the death of her best friend, Maria. This was until Amy convinced him to save the world, which made Shadow realize Maria doesn't want him to destroy it after all.
Merlina from Sonic and the Black Knight is a noticeable exception to the standard Big Bads in that she has a legitimately good desire but horribly misguided ways at going at it. She wants to prevent the fated destruction of the Arthurian kingdom. Her method of doing so, however, is to cast a spell of immortality upon the land that will cause the world to stagnate and plague it with monsters from the Underworld, and she's perfectly willing to kill Sonic if he stands in her way. She's also completely honest about helping Sonic defeat the corrupted King Arthur and save the kingdom as doing so will allow her to get her hands on his immortality-granting scabbard and ensure her plans of a "utopia". Sonic essentially spends their final battle having to beat it into her head with words and swords that her idea of "eternal salvation" isn't good for anyone in the long run.
Raphael is utterly devoted to Amy, a young girl who hid him from the French authorities after he killed a Evil Seed-corrupted noble in self-defence. After an encounter with Soul Edge which left him injured, he found to his horror that he was being transformed into a vampire-like creature, as well as Amy, who tended his wounds. His devotion to Amy, his need to protect her and provide the best for her turned psychotic, and coming to the conclusion that Amy could no longer fit into human society, he began infecting people and turning them into minions. He alternates between searching for Soul Edge and Soul Calibur to create a new world where they can live together happily.
As shown by Splatoon's Sunken Scrolls, Octarians are not a gratuitous Evil Counterpart Race of the Inklings. The war between them was over a territorial dispute, one that forced Octarians to take to the underground after their defeat. The reason behind their invasion is that the underground domes they call home are starting to fall apart, and they're starting to desperately need the electricity and territory.
The Ur-Quan. Especially the green Kzer-Za. Sure, they enslave other races and they're merciless to those who disobey them, but that's all due to their Freudian Excuse, which they will explain once you learn the Arc Words. In addition to their sympathetic backstory, they also seem to have a sense of honor; if you surrender to them, they promise to spare your crew. They are also willing to let you peacably leave their space (once) if you warn them about the return of the cause of their Freudian Excuse, regardless of you still being their enemy.
Their genocidal brethren, the Kohr-Ah, are less sympathetic...but since they share the same background, they may still qualify.
StarFlight: The Ancients, more familiar to the space community as Endurium, the fuel that powers starships, are committing genocide simply out of self-defense.
Juri from the Street Fighter series. While she is a psychopathic killer, in both games she appears in she is actively working to take down S.I.N. and Shadaloo. In Street Fighter V, she even saves Cammy and Decapre, two people she utterly loathes, before joining the heroes when they storm Bison's base.
Streets of Rage Remake, a fan-made condensation of the Streets of Rage series, has Rudra, a Canon Foreigner created specifically for the remake, who in-story is a mercenary ninja in the Syndicate's employ. Yes, she's a Dark Action Girl and a trained assassin, which isn't a completely noble profession to begin with, but circumstances reveal that she's with the Syndicate for a good reason. In her unique ending, it's revealed that the Syndicate was holding her little sister hostage, and the whole reason Rudra was working for them was so she could get the opportunity to free her sister. If you encounter her as a boss, following the fight she traps the heroes with a paralysis jutsu, only to inform them she's not their enemy before releasing them and fleeing. A combination of Types I and IV.
Suikoden II: There are a whole bunch of them on the Highland side of the war. The hero's best friend Jowy is the clearest example of this. In the end, both the hero and Jowy have the same goal, to ensure peace in the land. The problem is that they are leaders of opposing nations in a war in which one must wipe out the other to achieve peace, and they are also destined to do battle due to the nature of the runes they possess. Culgan and Seed are also anti-villains, and work along with Jowy and Leon (another anti-villain) to get rid of Luca Blight. Lucia also falls under this trope, as well as Kiba and Klaus, although they later join your party.
Suikoden V: Bahram Luger. He never wanted the bloodshed that the Godwins brought about, and he never wanted to face his mentor, Raja, in battle, but he holds his loyalty so high that he would suck it up and go do his duty.
To a lesser extent, Bowser himself qualifies. He's shown to be a loving father, all his minions adore him, and he's helped saved the world multiple times. Sure, those times were because he couldn't take over a world that doesn't exist, but he helped none the less.
Bian Zoldark from Super Robot Wars Original Generation (though apparently not in his original appearance in Super Robot Wars 2). He interrupts a secret peace talk between the government and some aliens, starting a war in the process, and creates the Divine Crusaders under the premise that the government planned to surrender to the invaders, and only by overthrowing them and uniting mankind can the Earth be saved. What he doesn't mention is that he knew all along that the aliens were actually planning to betray them and enslave humanity, and he certainly wouldn't mind it at all if a group of heroes showed up that were capable of defending the Earth themselves. He even goes out of his way to make sure the protagonists make it to their final battle with him.
In his previous appearances in Super Robot Wars 2 / 2G, his actions are also based on the knowledge that aliens will be coming to Earth and, as things currently stand, would have no problems annihilating it. Unlike in Original Generation however, the player and characters in game have no idea that the aliens in question even exist, and Bian's motivation appears to be based on world domination, which is not really helped by the company he keeps.
The Big Bad in almost ANY Tales Series game is an Anti-Villain, although some more than others, since they may be revealed at the end of the game or the last few hours.
Dhaos, the Big Bad of Tales of Phantasia, appears to be a ruthless Sealed Evil in a Can that aims to destroy all of mankind. However, after his defeat by the heroes, he regrets that it didn't have to end that way and reveals that he was actually the leader of an alien planet named Derris Kharlan, which had become ravaged by a great war and was slowly dying without a tree of mana to support it. In order to obtain a mana seed, he came to Aselia, but that planet's mana tree, Yggdrasil, was in danger of dying itself due to the development of Magitek. He attempted to warn the leaders of the research in Midgard, beseeching them to stop, but when that failed, he decided that Humans Are the Real Monsters and waged war on Midgard to force them to stop Magitek research. The heroes feel guilty, as they've effectively doomed Derris Kharlan by killing its would be savior. In the end, Martel, the spirit of Yggdrasil, transforms Dhaos' body into a mana seed and transports it to his home planet.
Tales of Destinys Hugo Gilchrist could count. Turns out, he's being possessed by the true Big Bad, Miktran/Kronos, to do every single one of his atrocities, and he only managed to save Rutee from being swept to the madness he's in, in the last moments of his sanity and could only tell everything just when he's on death's door. For that matter, a non-Big Bad example is Leon Magnus, who's only out for the safety of his surrogate mother figure, Marian, who's being used by a possessed Hugo as a bargaining chip. Yes, this occurs in both the original and remake version.
In Tales of Eternia, King Balirs wife Shizel claims to be removing all the negative emotions from the world by destroying Eternia, except this is more of a case of her being possessed by Nereid, the evil twin of Seyfert (what better for the God of destruction to favor if not saving the world by destroying it). Another set of twists involved her coming to her senses and using the Dark Fibril at the end instead of Meredy, thus saving her daughter's life.
Tales of the Abyss features many Anti Villains, even if they barely fit into this trope, considering that their idea of saving the world would wind up destroying it in the process. Notably, Van Grants wants to free the world from the influence of the Score, even though this involves him manipulating everyone and destroying the world.
Tales of Symphonia loves this trope. Almost every villain winds up being an Anti-Villain in their own way, even if some were moreso than others. Lord Mithos Yggdrasil simply wanted to end racism and get his sister back.
Tales of Legendia had this with the Ferines and the Raging Nerifes, the primary antagonists of the second half of the "Main quest". The game reveals that the Legacy dropped from another world and eventually became land. While it drops tantalizing hints throughout the game that that it was the Ferines that come from another world, at the very end, it is instead revealed by Maurits that the Ferines were the original inhabitants of the world of Tales of Legendia. It was the Oerines, the people of the land, who came on the legacy and created land at the cost of many Ferines' lives. Moses puts it best when he said, "We're the invaders?!" thanks to many events happening in the history of Legendia where the Oerines had waged war on the Ferines.
And in the character quest, Schwartz, the other half of Grune, was acting like she was just granting the desires of mankind.
Tales of Vesperia also uses this trope with the final Big Bad, Duke. While the first two Big Bads, Barbos and Alexei were just greedy and cruel, Duke becomes the Big Bad after deciding that Humans Are the Real Monsters thanks to the great war and Alexei stupidly summoning the Adephagos, and winds up acting like Shizel and deciding to save the planet and not the people.
Except that Duke also subverts it when he is actually just knocked unconscious instead of being defeated after a two to three stage battle, then when Duke comes to his senses, he actually sees eye to eye with the main protagonists of the game and then joins them and ends up saving the day instead of keeping his ideals to the very end.
Although much closer to being a "true" villain than Duke, even Alexei could still be considered this because, as he points out, his ultimate objectives are not all that different from Brave Vesperia's own objectives. Like them, he is attempting to end the Empire's stagnation and the various other problems in the world. The primary difference is that while Yuri is willing to use almost any means to reach his goals while working as a free man, and Flynn upholds Imperial law while attempting to reform the Empire from within, Alexei uses any and all means available to him, including resources outside of the Empire's sphere of influence. What cements him as this trope best is his own appeal to the party: "Not ONE of you believes the Empire is in the right!"
Tales of Zestiria again with the Big Bad, Heldalf. While Heldalf was a bad person before his transformation into the Lord of Calamity, it was mundane evil. He took over Camlann, the Origin Village, to secure a route from his homeland, the Rolance Empire, to prepare for an invasion of the Kingdom of Hyland. When Hyland forces invaded and slaughtered the village, he simply withdrew his troops. When the chaos corrupted the God who lived there, Maotelus, as well as the previous Shepherd's newborn child, the Shepherd sacrificed his child to the corrupted Maotelus to curse Heldalf to live a live of unending loneliness and pain, thus turning him into the Lord of Calamity, who sought to turn all humans into hellions to reveal their true nature.
And the Big Bad of Tales of Berseria, Artorius Collbrande, as well. When humans who gave into their malevolence turned into daemons on the Scarlet Night, and killed his wife and unborn child, his heart was filled with despair. This turned out to be the first step to awakening Inominat, who would surpress humanities' emotions to stop the creation of daemons. At this point, he was approached by Melchior, who convinced him to lock away his emotions and work to revive Inominate for the greater good, and seven years later, he sacrificed the protagonist, Velvet Crowe's, brother, Laphicet, which ended with Velvet transformed into a daemon and set off the events of the game.
Anna Williams, like her sister Nina, is an assassin with a violent mutual grudge against her sibling. Unlike Nina, there are many strong hints that Anna wishes it didn't have to be that way, and she has tried a few times to end their feud, with no success.
Kunimitsu started out as a self-serving thief who was expelled from the Manji clan, but gave up her criminal ways to make an honest living as, of all things, an AC repair technician. She returned to thievery to get hold of Yoshimitsu's prized sword, but her motive for doing so is not personal gain, but to please her dying grandfather, and Yoshimitsu now seems to regard her as a Worthy Opponent rather than an Arch-Enemy (after the more straightforwardly villainous Bryan Fury subsumed that role from her by slaughtering the rest of Yoshimitsu's clan).
Jin Kazama and Kazuya Mishima both started out as noble young men, but have fallen to an actual genetic predisposition toward evil that neither can fully control. Kazuya embraced this at an early age, but for Jin it was more of a hostile takeover.
In 6, Jin seems to go completely off the deep-end and starts a war against the world to seemingly take it over. In fact, it's all part of a plan to awaken a demonic being, Azazel, who is foretold to bring about the end of all mankind when the world is embroiled in chaos, so he can kill the beast once and for all. His intentions are good, but he still causes a massive war in which many, many people die. And because he's in a coma at the end of it, come 7, the war is still raging and the devastation is immense.
Yuyuko Saigyouji found a body sealed under the Saigyou Ayakashi, a great cherry-blossom tree situated in the realm of the dead, and, driven by an intense curiosity, had her bodyguard steal the essence of spring in order to break the seal preventing the tree from blooming and using it to revive the body... only to find out, at the last possible second, that Ghost Amnesia had lead her to forget that the body sealed under the tree was her, that she died in order to seal the tree,a soul-eating abomination and one of the few unambiguously evil entities in Touhou.
You don't even have to be a final boss to qualify for this trope in Touhou: Parsee Mizuhashi is a Hashihime, a Bridge Princess, a youkai incarnating envy and jealousy, and the guardian of the bridge leading into Hell who attacks anyone that passes her by. Not necessarily because it's her job, but much more so because of how jealous she is of them... Are they happy? Well, that's clearly enviable. Are they unhappy? Well, at least they can still walk about in the sun. Are they miserable? Well, at least they have the forebearance not to envy those who have it better than them. Are they envious of those who have better of than them? Well, seems they've just given Parsee the sustience she needs to overpower them.
Even though she wasn't evil, Utsuho was still one of the darkest Touhou villains to date... So, to compensate, the next game's final boss was Byakuren "Youkai Jesus" Hijiri, a Buddhist nun who was sealed in the Demon Realm for thinking that it would be nice if humans and youkai could get along... She's not a villain by any stretch of the word. In fact, it wouldn't be uncalled for to accuse the heroes, the playable characters, of meeting the criterias for Nominal Heroes when they set out to prevent her followers from freeing her.
Junko serves as a particularily Vile Villain in Touhou, having set out to commit genocide on the Lunarians just to get back at one of them, Chang'e, for something her husband, Hou'yi, who Junko has already killed, did... So what did Hou'yi do to motivate such an all-encompassing revenge? Well, he killed his and Junko's son... and the grief drove Junko mad, leading her to turn her power of purification upon herself, cleansing herself of everything aside from her feelings of resentment: Her grudge towards everything associated with Hou'yi is all she has left now, and she, herself, is little more than a woman consumed by her own rancor who lashes out in pure fury at those she holds responsible for her misery.
The Trails Series has a few characters that could be called as this. Due to the series being a Long Runner and the fact that it's been released in the west, the Sky series will not be spoiler tagged.
The Legend of Heroes: Trails in the Sky FC has Alan Richard who wanted to bolster his nation of Liberl to make it into a military nation strong enough to withstand the might of the Erebonian empire after they were invaded by Erebonia fourteen years before the start of the storyline. Part of this is because of his hero worship of the protagonist's father who was a legendary commander who retired from the army after his wife died from the war. At the end of FC, Cassius calls him out on it by claiming that Cassius in the end is just one guy and he can't do everything.
Its sequel SC has Loewe, one of Ouroboros' strongest Enforcers and the older brother of Joshua (though they have no relation with each other biologically; rather, he was the boyfriend of Joshua's older sister.) A victim of the Hamel Incident of the empire that started the Hundred Days War between Liberl and Erebonia, he allied himself with Ouroboros to judge humanity using the Aureole and the Liber Ark to see if humanity can actually work together in a time of crisis. Joshua ultimately calls him out on this in their final duel where Loewe in the end is still hung up on Karin's sacrifice and calls him out by saying that Joshua himself is proof of everything that Loewe's been searching for all this time. Loewe loses the duel and actually thinks of quitting Ouroboros when he's struck down by the Big Bad. He still manages to go out in style due to him disabling the barrier used by the Big Bad.
In Ao no Kiseki, it's revealed that Ian Grimwood is this because of what had happened to him in the past where his wife and son died due to the plane they were on crashed thanks to the intelligence war between Erebonia and Calvard, two nations that want Crossbell City because of how rich the city is and yet has no military manpower. He wants to create space for Crossbell in order to no longer look weak in comparison to the two nations. Unfortunately, he had to kill the protagonist's older brother who somehow managed to find out about the conspiracy way early to keep things secretive. Dieter Crois and Arios MacLaine are also these to a lesser extent, mostly for the same reason Ian has.
In The Legend of Heroes: Trails of Cold Steel, Giliath Osborne is revealed to be this especially in III and IV where he wants to get rid of the curse of Erebonia that's been plaguing the empire for good. Unfortunately for the heroes, he has to first kill the Divine Beast that is holding the curse at bay and has to sacrifice the Artificial Human that is Rean's student to transform her into the sword that allows anyone to kill the goddess Aidios' beast sent to guard her treasures, the Sept-Terrion. At the end of III, Millium takes Altina's place and sacrifices her life to become Rean's sword who then gets swallowed up by the curse and hacks the Nameless One in rage.
King Asgore of Undertale has declared war on all humans, giving hope to the monsters trapped in Mt. Ebott that they can one day return to the surface and enact their revenge for being sealed. Asgore made that declaration in a fit of anger after the death of his son Asriel and his adopted human child, both of which humans were responsible for. Asgore has regretted it ever since, but is forced to keep up the ruse because otherwise his people would lose all hope and fall down. When the player reaches Asgore in a boss battle, it's clear he really doesn't want to go through with killing the player, but feels he has no choice.
Vagrant Story's Sydney Losstarot is actively trying to seal away Leá Monde, so as to defend it from the power-mad Cardinal and his Knight Templar, Romeo Guilderstern. The entire game is a Batman Gambit to have Ashley inherit all the power of the city and then willingly disappear from the world.
In Verdict: Guilty!, none of the criminal playables is really evil; they're either innocent, doing it for a good cause, or being duped by the real villain.
The Walking Dead: All through the game, you're led to believe that the Voice On The Radio is a manipulative bandit, or paedophile, or psycho-killer, or some other sort of monster of a human being. He's not. Remember that car full of supplies your party looted back in Episode 2? The one everyone thought was abandoned? It wasn't. At the end of it all, the terrifying, overarching Big Bad that had been built up over three Episodes was nothing more than a severely traumatised survivor who was just trying to look after his family until they were all killed in a Despair Event Horizon that you were directly responsible for causing.
Before The Burning Crusadederailed his character into a one-dimensional madman (and then later Legion retconned it into a successful deception by the... erm, Legion, in order to get the players to kill him), Illidan Stormrage of Warcraft spent much of Warcraft III as one of these after consuming the Skull of Gul'dan and turning into a half-demon, half-night elf hybrid. He goes through the rest of his appearances using increasingly-dangerous and morally-questionable means to fulfill his goals, allies with the series Big Bads, the Burning Legion, and nearly causes massive ecological devastation by using a powerful artifact to fire a spell at the Frozen Throne before being stopped by Furion and Tyrande. And the reason why? He wanted to prove to Tyrande and his brother that he had been rehabilitated and wanted to help, but kept thinking he needed just a little more power to do so. In addition, his sympathetic backstory as the Cain to Malfurion's Abel helps cement his status as an antivillain. No matter how well intentioned or well thought out, or even if he accomplished his goals, he was always considered a "failure" compared to his brother during the events of the War of the Ancients.
Cocytus member Ptolomea is A Father to His Men, and has a strong streak of honor to him even as he's cooperating in committing acts of terrorism. When he finally dies, his last request to his adversaries is trying to protect the lives of his men.
Liz and Ard have ulterior motives for working with Odessa, in that they believe it will help them repair their spaceship so they can return home.
Irving Vold Valeria is finally revealed to be The Chessmaster of most of the game's events, having founded and bankrolled Odessa's operations while simultaneously doing the same for ARMS, in an elaborate gambit to force Filgaia to somehow mobilize all its resources to get ready to fight against an approaching Eldritch Abomination gradually devouring the universe.
Virtually every human opponent in the Xenosaga series.
Each of the Testaments has their own reason for supporting Wilhelm's manipulations of the universe's time-space. Albedo wants to protect Jr. from Yuriev incarnate in Nigredo; Virgil wants to be reunited with a Realian who taught him compassion, Febronia; and Kevin wants to be reunited with his dead mother and Shion. Voyager, however, is still a prick.
The Ormus group consisting of Pellegri, Margulis, Herman, and Richard fights to avenge their destroyed homeland and protect the ancient relics that power humanity's exploration of the universe.
Wilhelm seeks to initiate an Eternal Recurrence and prevent the universe from disappearing.
Xenogears, spiritual ancestor to the above, also shares the proclivity.
Ramses fights to justify his existence despite having been made obsolete at birth by Fei's incarnation.
Krelian wants to bring about an Assimilation Plot and end suffering and separation between humans.
Despite being the first villains introduced, the members of Torna actually end up serving an anti-villain role in the grand scheme of Xenoblade Chronicles 2. They are smaller, less influential, and all motivated to stop Amalthus, who has more reason to being called the main villain of the game
Toal Fact in Ys Origin. Yes, he joined up with the invading demon army, fought against his brother and former comrades, and even accepted a demonic element into himself, but it was all a ploy to destroy the Black Pearl and prevent the Goddesses from sacrificing themselves. Unfortunately, it didn't work out quite like he had hoped.
The Jester in Zork Zero is a persistent thorn in your side, appearing out of nowhere to play stupid practical jokes on you, much like his earlier counterpart the Wizard of Frobozz. Not only does dealing with him take precious time, but his tricks can sometimes get you flat-out killed if he randomly shows up during a timed sequence. Unlike the Wizard, the Jester is not actually trying to stop you; he's a Trickster Mentor. He is Megaboz, and his goal is to sweep away the remnants of the corrupt and evil Flathead Dynasty. Unfortunately, he goes about this noble goal in the most irritating and extra way possible.