Matsuda. He's your classic Idiot Hero — impulsive, well-meaning, slightly self-centered everyman who's ultimately devoted to his True Companions. He spends the whole series opposing a serial killer, since he is a cop. He just so happens to be working against Villain Protagonist Light. If you rewrote the entire series to be from Matsuda and L's perspective instead of Light and Misa's, with only short ventures into their perspectives as L and Matsuda were given, the whole series would still mostly work, especially since Matsuda's behavior usually makes an interesting and vital contribution to the story, like stumbling on Yotsuba and shooting Light.
Soichiro until towards the end, and he is described by the author as the only one-hundred-percent good character. However neither of them are Light's direct antagonist as such, while L and Near are.
A few of the Marine Officers the main characters have to face are genuinely good guys who actually want to protect that public and don't view civilians and their own soldiers as being completely expendable. Notable examples are Smoker, Tashigi, T-Bone, Coby, Garp, and Aokiji.
One filler arc included the presence of a rational, normal Marine captain, who had no strange abilities or quirks, but was led by some crazy, immensely fat admiral and his equally stupid lieutenant, who where on par with all the early, lighter One Piece villians.
Commander Jonathan of the G8 filler arc also provides an example. While he pursues the Straw Hats after they literally drop into the middle of his fortress, he offers mercy to the crewmembers that don't yet have bounties, refuses to treat his men as expendable, and has nothing but disdain for the visiting commanding officer that wants the Straw Hats captured no matter the cost.
Also Magellan and Hannyabal, the chief warden and vice-chief warden of Impel Down. Their motives are basically to stop the prison break (which was initiated by Luffy) and keep order in the prison. Considering that most of the people in Impel Down deserve to be there (and would terrorize citizens if they escaped), you could make a very convincing argument that Luffy is more of a villain during the Impel Down arc are than Magellan or Hannyabal. After all, Luffy is putting his desire to save his brother over the well-being of the rest of the world.
In Ghost in the Shell: Stand Alone Complex, there are the soldiers who storm and arrest the members of Section 9 - they're very much aware of what they're doing, so they're not Inspector Javert, but they are approved by the city and they limit the use of lethal force. Heck, the Laughing Man (SAC), Hideo Kuze (2nd GIG), the Puppeteer (Solid State Society) and the Puppetmaster (1995 Movie) also qualify to some extend or for limited periods of time.
Cosmo Entelechia as well, though somewhat more dickish about it than necessary. Ultimate plan? Save over a billion lives. Opposed by? First an idiot hero who doesn't know what he's really doing and twenty years later a child. To be fair to the idiot hero, Nagi, a lot of what they were doing just doesn't make sense when considering their ultimate goal.
The Wolkenritter in Magical Girl Lyrical Nanoha A's. So here we have a group of "villains" whose malicious goal for filling up the Artifact of Doom was so they can save an innocent Ill Girl from certain death, and they were doing it in a way so they wouldn't kill or severely maim anyone. Problem was, due to reasons beyond their control, it wouldn't have worked without Nanoha's help. Either the Book of Darkness would have killed the girl and reincarnated elsewhere, or Admiral Graham would have frozen them both forever.
Inspector Runge from Monster starts out as one, though he turns to more of a standard villain for a while as his search more Tenma becomes more of a personal obsession than anything to do with justice, causing him to ignore the increasing evidence that Johan does exist. However, he eventually comes to his senses and becomes a hero again.
Also Eva Heinemann, whose Rich Bitch front and vengeful personality, as well as her contention that "not everyone is equal," belies her desire for a more fulfilling life. When given a choice between helping Roberto end Tenma's life or helping Tenma escape and survive, she chooses the latter, and, later in the series, her character development allows her the opportunity to work beyond her grudge, do the right thing and become a better person.
Zechs Merquise from Gundam Wing; after achieving his initial goal of revenge for the destruction of his homeland and the murder of his parents, sets about trying to realize their goal of a peaceful world - the exact same goal his sister Relena, the show's female lead, is going for. The major difference is that Zechs is a Well-Intentioned Extremist more than willing to hold the Villain Ball in order to scare the planet towards peace - and his personal pride keeps drawing him into battles with protagonist Heero.
Bleach: The entire Seireitei (sans Aizen and company) in the Soul Society arc, if you look at it from their point of view — they're giving out lawful punishment to a criminal, and Ichigo and friends are the equivalent of an armed mob raiding the police station to break her out.
The court in Seirei No Moribito. They only want to destroy the water demon that will cause a drought in the land, and none of them are very happy about the fact that the host has to die to do it. It's not really their fault that they don't know the true nature of the possession. They learn otherwise, which ends up aligning them with the heroes instead.
Since Ryuhou and Kazuma get about equal screen time, Ryuhou is a joint protagonist—several episodes focus on his perspective. He evolves into a protagonist in the episodes following his second battle with Kazuma, but up until then he's just painted as a semi-peaceful well-meaning villain.
Alexander Anderson and the Vatican in general. Anderson's a Sociopathic Hero, sure, but it's about the best you can get in Hellsing anyway.
Vatican Section XIII, the Iscariot Organization to which Anderson belongs, goes well off the deep end in the manga by waging another crusade on both Millenium and all of England, swinging them into literal Knight Templar territory. This actually highlights Anderson's own moral compass because he assists in killing his boss for his crimes.
Granted, even that fails to make them worse than the protagonists.
Team Unicorn and Team Ragnarok of Yu-Gi-Oh 5Ds. But at least the protagonists aren't that bad.
Kira Yamato qualifies as one in Gundam SEED Destiny, against the Anti-Hero Shinn Asuka, until the supposed role switch after the destruction of Freedom Gundam.
The Allied Forces in Axis Powers Hetalia could be seen this way. The Axis has the sympathetic POV.
Kamikaze Kaitou Jeanne has Miyako, her best friend and pursuer, and Chiaki/Sinbad, who tries to stop her from helping the Devil because he is working for God all along.
In the first arc after the Time Skip in Tengen Toppa Gurren Lagann, Rossiu ends up sentencing Simon to death and abandoning a large proportion of the Earth's population to probable death in order to protect the peace and then the world. They also become kind of a prick. Though torn by guilt, no one condemns them, except the less rational good guys and many fans - though in the latter case it's mostly due to the character's becoming kind of a prick.
By the end of Shakugan no Shana, Yuji Sakai with Snake of the Festival are this trope. They get to save the world and make the Flame Haze the bad guys without them knowing it.
Oswald/Glen Baskerville of Pandora Hearts has revealed himself to be this and only wants to reverse the effects of what he believes his own naivety caused one hundred years ago. By going through with his plan to travel back in time and kill Lacie before she can give birth to Alice and the Will of the Abyss and incite the creation of B-rabbit Oz, he would erase a good many characters from the timeline but would also prevent the deaths of countless innocents. Unsurprisingly, Grey and Gray Morality abounds in this series.
Elfen Lied: Has a few, as one protagonist is a mass murderer who even killed the other Protagonist's sister and father.
Kurama does some things of questionable morality, but he wants to control and study the Diiclonius virus, in part to help others so their children don't turn into murderous psychos. His vendetta against Lucy, however, is more personal, as is her hatred of him.
Shirakawa initially a cold Girl Friday to Kurama, secretly she investigates the Director, and seeks to stop his experiments. Even after her death, her information informs her superiors, the Japanese Government of the experiments at the facility and they mobilize against the Director.
The Operatives they hate Lucy, and they pilot the vector craft to attack the facility kill any and all Diiclonius, and retrieve the cure to the disease, which has just been used to infect everyone in the world. They have no problems with lying and shooting unarmed people as long as they complete their task.
The Agent is one as well. Initially just a replacement field operative after Bando and The Unknown man were indispose. She wants to save the world from the diiclonius virus. She opposes the protagonists, but honestly does not care about them, as they're all small in the grand scheme of things. She rescues Arakawa, who has the cure, and risks her own life to get the scientist to safety. Her motivations are notably without the self interest that almost every other character has, she just wants to do the right thing.
Argent the Wolf of Grendel, who's opposed to the Villain Protagonist Grendel (particularly Hunter Rose, but later on Christine Spar) as an Anti-Hero Werewolf who is compelled to take down what the series equates to the Devil.
The U.S. military is usually portrayed this way in The Hulk, as they usually genuinely believe that the Hulk is a dangerous monster that they need to stop. Stan Lee commented in an interview that portraying them that way allowed him to get around the Comics Code insistence that authority figures always be portrayed positively. Lately this has changed, there has been a trend to portray General Ross, who usually commands the anti-Hulk military forces, as a General Ripper.
In Empowered, most of Emp's jerkass teammates qualify, particularly Sister Spooky (although she becomes more sympathetic and less hostile towards Emp in the later volumes).
An early installment of Tintin has Nestor the butler as this. He's working for someone he doesn't know is evil, and for much of the plot he actively sabotages Tintin and the Captain.
Ord from Whedon's "Breakworld" arc in X-Men. He seems like an Always Chaotic Evil alien invader at first, but ultimately he's just trying to save his world from destruction. The only reason he is even opposing mutantkind in the first place is because of a prophecy planted by the real Big Bad that a mutant would destroy Breakworld. In the end, he makes a Heroic Sacrifice to save Breakworld from the true Big Bad.
Averted with Numbuh 86 in Captainwii's Operation: REBEL, where she hunts down 3 fugitives to give them Laser-Guided Amnesia, while she is working with the KND, a typically good organization, the fugitives are trying to escape her, being convinced that as long as they don't turn evil and betray the KND, that they should have right to keep their KND memories. Also this trope can be considered averted considering that Numbuh 86 isn't exactly a nice person
Clopin actually becomes one near the end of The Hunchback of Notre Dame. Yes, everyone's favorite Gypsy king and master of ceremonies, who is often cheerful and friendly, and suddenly become a cruel judge presiding over a Joker Jury in the Court of Miracles!
US Marshal Sam Gerard (Tommy Lee Jones in the role that made him famous): The Fugitive. His quest is to capture the hero, who is a fugitive from justice, whether or not he's innocent of the charge. The character was popular enough to warrent a spin-off sequel, U.S. Marshals, which goes through a similar premise, but is actually starring Gerard.
Colin Farrel's FBI Agent brought in to investigate Pre-Crime in Minority Report.
Martin Prendergast in Falling Down. Unlike Bill Foster, who is on his violent rampage against the petty frustrations of modern society, Det. Prendergast tracks him down while constructively dealing with his own annoyances with empathy and maturity.
Most of the colonial officers and men (such as Commodore Norrington) that oppose Jack Sparrow throughout the Pirates Of The Caribbean films, since they are technically trying to bring a wanted criminal to justice. Cutler Beckett is a total bastard though.
Iceman from Top Gun. He's a git, but he's on our side. He even has a point regarding Maverick being too dangerous. Really, all he wants is what's best for the navy.
Antoine Richis, in Perfume, played by Alan Rickman. Richis is an intelligent nobleman and loving father who tries to protect the city and his beautiful daughter from the protagonist, a serial killer who preys on virginal girls.
Brad Pitt's team in Inglourious Basterds are presented in this way, as for most of the movie, we are either following around their enemy Col. Landa or an entirely different plot.
The Medjai function this way, at least at first, in The Mummy. While they attack the protagonists, it's only to stop them from awakening Imhotep.
Ditto for Kazim in Indiana Jones and the Last Crusade. He doesn't know Indy's intentions and just wants to protect the grail from falling into the wrong hands, and when the misunderstanding is cleared up, he helps out.
Jack Welles from Takers. While the bank robbers were the Villain Protagonists, he's a cop trying to stop them.
FBI Special Agent Adam Frawley fulfills this role in The Town. While he was very much a Jerk Ass and not quite as personally sympathetic as the Villain Protagonists, he was ultimately an FBI agent trying to shut down a ruthless and dangerous gang of bank robbers.
The Negotiator. Kevin Spacey plays a negotiator who tries to negotiate another (rogue) negotiator (protagonist Samuel L Jackson) out of doing something dumb after he holds up some hostages because he was framed for murdering his partner. As far as Spacey is concerned, Jackson is armed, has hostages and is therefore the villain.
The policeman Mitch from First Blood. Unlike the other cops he didn't bully Rambo, but still participated in the hunt for him. To a lesser degree, Col. Trautman, who knows and understands Rambo, and wants him brought in without bloodshed (partly because he alone knows just how much bloodshed will result).
The titular detective from Columbo was depicted this way in his initial appearance in ''Prescription Murder, the main Sympathetic P.O.V. being on the culprit with the detective not appearing till near halfway through the movie. However the series began developing Columbo's trademark whimsy and wise cracking persona afterwards and, while a lot of spotlight is still usually given to the suspects, Columbo eventually became the lead.
Tommy Conlon in Warrior. He opposed the protagonist for reasons unknown until the very end, an example of Good Versus Good.
The title character of the old western film Chato's Land, played by Charles Bronson. He is also The Voiceless, having only two speaking scenes in the entire movie – one, extremely brief, at the beginning, and one later in the film, shot entirely in the Comanche language, with no subtitles.
Pamela Landy in The Bourne Supremacy. In the next film, The Bourne Ultimatum, however, she helps blow the whistle on Operation Blackbriar.
The Winkelvoss twins and Divya Narenda in The Social Network. They're both snobs (Narenda being the Token Good Teammate), but the film depicts them as being in the right, since Mark did steal their idea.
The police chasing Maindrian pace in Gone In Sixty Seconds 1974. They're only trying to put a stop to a recent rash of high end car thefts.
The guards in Escape From Alcatraz, who are simply trying to contain a prison full of dangerous criminals. The only completely unsympathetic "good" character in the film is the Warden.
Morgan from The Dresden Files, who watches Harry like a hawk, convinced that he's either a traitor to the White Council or just into Black Magic. At the same time, he's a warrior who will do anything to stop evil and protect the innocent. Eventually, he gets over his distrust of Harry; he still thinks Harry's a loose cannon, sure (and he's not exactly wrong, either), but he sees that Harry's trying to do good. Then, he dies.
Kariya Matou in Fate Zero. His reason for entering the Grail War and deciding to endure horrible torture and surely die no more than two weeks after the Grail War ends to make up for his lack of training? Because he's the Unlucky Childhood Friend of Tokiomi Tohsaka's wife and he wants to save her daughter, because he knows pretty well what kind of magecraft the Makiri family perfected. Oh, and since he failed, just look what happened to Sakura in Heaven's Feel Route. Granted, his ending and last couple of actions aren't exactly very heroic, but yea, the motive was good.
Duke Michael in The Prisoner of Zenda. Unquestionably a better person and ruler than the legitimate king, and almost as good as the main character.
Also a plot point in Witches Abroad, in which wicked witch Granny Weatherwax is the one aiming to stop a fairy godmother trying to force storybook endings onto people. During their encounter, said godmother insists that she's the Good One.
Played with in The Truth, in which the protagonist William de Worde (mind you, not a Villain Protagonist) finds his work as a journalist significalty complicated by one Sir Samuel Vimes, Commander of the City Watch. Most readers will know Vimes to be a thoroughly decent, if perpetually grumpy, person and, as such, can understand where he's coming from.
Moist von Lipwig has a similar relationship with Vimes. Lipwig is a criminal, and Vimes has every reason to be suspicious of him, but in this case he's actually attempting to accomplish something good.
After Lebel is introduced, the plot stops following the Jackal exclusively, and is as much Lebel's story as it is the Jackal's, so Lebel goes back and forth between being a Hero Antagonist, and a straight Hero. The Jackal goes back and forth between being a straight Villain and a Villain Protagonist.
Ged, the protagonist from A Wizard Of Earthsea, serves as the Hero Antagonist to Tenar in the follow up book, The Tombs of Atuan. Tenar spends the entire book as a priestess to a cabal of evil spirits posing as gods, and when Ged clues her into that fact, she Heel Face Turns and sides with him—much to the chagrin of her old bosses.
Thot Keer from Star Trek Typhon Pact — Zero-Sum Game. A Breen shipyard manager, his work crews are developing a prototype starship using stolen Federation technology, and the protagonist's mission is to destroy both prototype and shipyard. Keer is certainly not a villain, though; he is merely a patriot who takes pride in his work, and displays great bravery and (for want of a better term) humanity throughout the novel.
In the same series, Praetor Gell Kamemor is a Romulan patriot opposed to the Federation politically, but she adamantly disagrees with the notion of Romulan superiority promoted by the Tal Shiar and much of the military. She would rather resolve the conflict with the Federation in the diplomatic arena than on a battlefield. All of her scenes in the series show her as a Reasonable Authority Figure compared to the previous cadre of conniving and backstabbing Romulan politicians.
The entire Jedi Order plays this role in the Darth Bane trillogy as the books focus on the perspective of the titular Sith Lord and his apprentice Zannah.
Roy Merritt in Daemon. Though we eventually know better, Sobol is a dangerous maniac who employs a menagerie of vicious sociopaths.
Porfiry Petrovich, the brilliant and implacable policeman investigating Raskolnikov, in Crime and Punishment.
There are multiple examples in Dexter, all in opposition to Dexter, the serial killer protagonist.
Sergeant Doakes, though his morality is called into question a few times. Somehow, he's the only one in a precinct full of cops and forensic specialists to get a creepy vibe off serial killer protagonist Dexter. This doesn't end well for him. When he discovers that Dexter is a serial killer in season 2, Dexter locks him up in a remote cabin. Then Doakes is killed by a woman who was obsessed with Dexter and tries to cover up for him.
Special Agent Frank Lundy in the second season of the same. He probably would have caught Dexter if it weren't for Doakes' suspicious and secretive behavior making him more conspicuous than Dexter.
Detective Quinn is set up as this in season 5. He's the only one in the office who notices that the Mitchell family's sketch drawings of "Kyle Butler" look a lot like Dexter, and starts to suspect that Dexter may have killed Rita, his wife. At the end of the season, he abandons his investigation when Dexter gets him off the hook for a murder that Quinn is erronously suspected of (in fact, Dexter himself committed the murder), and he falls in love with Debra.
Stan Liddy in season 5 as well. Although he's a Dirty Cop, and is trying to expose Dexter mostly for his own benefits so that he will be reinducted into the police force, he is still trying to catch a serial killer. Dexter kills him, and Quinn is subsequently suspected of the murder.
Maria Laguerta in season 7. She discovers evidence that may expose Dexter as the real Bay Harbor Butcher, and starts her own investigation. Dexter dismantles her case by setting her up as looking like she has an irrational grudge against Dexter instead of solid evidence. Dexter then tries to kill her to get rid of her permanently, but Debra intervenes. She shoots LaGuerta to cover up for her brother.
Jack Walters, Joanne Meltzer, and later, Jeffery Sykes on Profit.
Most of the less-developed alliance officers in Firefly qualify as this.
Word Of God (see the commentary track for Serenity) is that the Alliance as an organization is not evil, it's just plagued with idiot optimism and thinks it can make people better.
... granted, everything we ever see them do ranges from evil to indifferent (but hostile). Maybe this counts as Offscreen Heroism?
Consider the fact that life on the core worlds appears to be really good, with clean cities and top-notch health care. Much of the series concentrates on the relatively undeveloped border worlds where Alliance tactics can appear somewhat brutal, but out there the Alliance faces bandits, pirates, and reavers. In those circumstances, brutal is a better option if it means they can protect civilians.
In the second season of Dollhouse, Senator Daniel Perrin is definitely this as he tries to expose the corrupt Rossum corporation, the Dollhouse's main benefactor. Until it turns out that he's a Doll imprinted to investigate the Dollhouse so that he can "discover" convincing evidence that it doesn't exist and exonerate Rossum.
Many of the antagonists in Merlin are just working to bring down King Uther, who is undoubtably a tyrant.
Arthur occasionally lapses into this. While he's undoubtedly The Hero, he has been raised from birth to be distrustful of magic and will not hestitate to arrest anyone caught using it, even though the penalty is death. What seperates him from Uther is that he does this not out of maliciousness, but because it is his Father's law and he's honour bound to obey it.
Agent Hank Schrader of Breaking Bad. Something of an interesting case in that he doesn't know the Villain Protagonist he's chasing is his own brother-in-law...until the middle of the finale season.
In the Angel episode "Sanctuary" Buffy becomes this. She wants to kill Faith; it doesn't matter if Angel wants to redeem her. The former lovers even come to blows because of it, and part on bad terms.
Lee Jin Pyo in The City Hunter: His entire black ops team was murdered by their own government,who first denied their existence and then branded them as traitors. As he's a "dead man," he can't work/live in his native Korea. He just wants to expose their corruption and get revenge on the ones who ordered his team's execution.
CTU whenever Jack Bauer has to go rogue or is set up on 24 (which is a lot)
Wizard Of Waverly Place is pretty much driven by the fact the three protagonists are that for each other. Even so with Alex, whose the nearest the serie have to a reccurring main villain, and his by-the-book brother Justin.
Person of Interest: Detective Carter is actively trying to track Reese down...for the first few episodes, anyway.
Scandal: First Lady Mellie Grant floats in and out of this role.
Older Than Feudalism: Hector. There are a number of scholars who believe that The Iliad is the tragedy of Hector, not Achilles. They cite as evidence the facts that the Trojans are portrayed far more sympathetically than the Greeks, Achilles finding redemption instead of punishment at the end, and the fact that the narrative ends with Hector's funeral.
Dante went so far as to place Hector in Limbo (the nicest place a pre-Christian could end up) in The Divine Comedy, and he became part of the Nine Worthies, nine personifications of Chivalrous behaviour, during the Medieval ages (mind you, the other pagan "Worthies" were Julius Caesar and Alexander, whose "chivalry" should probably be taken with a grain of salt). History certainly treated Hector better than it did most of the invading Greeks, due to the perception of him as a noble man trying to defend his home over his brother's folly and the Greeks' warmongering.
Dante was of the belief that the Trojans were the ancestors of the Roman founders and the Julio-Claudian dynasty— who in turn were the ancestors of Italians, particularly the Florentines. This colors his attitude somewhat, such as placing Ulysses and Diomedes deep in Hell for the Trojan Horse gambit.
Agent Edgar Ross from Red Dead Redemption. At the core, he wants to bring law, order, and civilization as well as round up all those who seek to destroy it. Were he not the antagonist, we would likely think he's onto something, perhaps even root for him in secret.
Cyrus Temple from Saints Row The Third. His evil plot? To restore order by stopping gang wars. You are a member of a gang, and thus that makes him the antagonist. Were this any other game, he'd be the good guy.
In Deus Ex, after you defect from UNATCO, any cop or U.S. or UNATCO soldier that truly believes he is fighting for the greater good and is not flat out sadistic or part of the conspiracy, fit this trope.
Ash Crimson from The King Of Fighters series. His actions make him a villain, but in the end, it's for the sake of stopping an even greater evil, who happens to be the final boss of KOF XIII.
Hakumen from BlazBlue, one of the Six Legendary Heroes who saved the world from the attack of The Black beast. He wants to prevent a rebirth of The Black Beast by killing Ragna. He is not open to alternative solutions.
In the end of the sequel, the mantle of Hero Antagonist goes to Litchi Faye-Ling. She's still the same kind-hearted woman, but opposes Ragna because Ragna's opposition (NOL) took captive of her love interest, and a Troll convinced her thoroughly that they have a mean to restore said interest. To top it all off, she's dying because she was exposed to the same thing he was (dying is a better case, the worst case is, she turns into the same monster that her love interest becomes and consumes everything in her path, including the innocents she grew to love), and anyone who could help her refuses to. She's reluctant to fight for that evil organization, but she really didn't have a better option.
Jowy Atreides, from Suikoden II. A long time friend of the main hero, Riou, he is destined to come into conflict due to picking up opposing runes (Jowy picks up the Black Sword Rune and Riou the Bright Shield Rune). Jowy ends up betraying and murdering (although not willingly) the mayor of Muse, Anabelle. He ends up becoming king of Highland. He ends up as a Hero Antagonist because he helps bring down Luca Blight, as well as using his strength to keep the Beast Rune at bay. He ends up having the same goals as Riou, to end the war and to unify the land. The problem is that he and his friend, Riou, lead opposing forces. His love of the orphan Pilika truly drives Jowy in his goals for peace.
Thorndyke from Soul Nomad. Also, everyone but the monsters in the Demon Path.
Harpuia from Mega Man Zero. He even prefers to be destroyed than to be possessed by a manifestation of evil in the second game.
By extension, Harpuia's fellow Guardians, Leviathan, Fefnir and Phantom, as well as all of the Bosses prior to Zero 3, fit this trope. They were only following orders for the sake of protecting humanity.
Knuckles in certain Sonic the Hedgehog games, in particular those where he is tricked by Dr Eggman into stopping Sonic. He eventually realises he has been duped, and usually reverts to a side protagonist for the remainder of the story.
Velvet from Odin Sphere, against both Ragnanival and Ringford. Given Gwendolyn and Mercedes are guilty of most of the incidents of Nice Job Breaking It, Hero in the story (Velvet causes very little herself), she's rather justified.
Gordon Freeman and Cpl Adrian Shepherd are the protagonists of different Half-Life games, working to opposing ends. Shep wants to catch Freeman, for starters, and Freeman has nuked a number of soldiers.
Subverted in Disgaea 3. Mao is a Villain Protagonist (Noble Demon type), and Super Hero Aurum is originally portrayed as some legendary super hero. The subversion occurs around Chapter 8, when the player discovers that Aurum is nothing but a big phony who's so foul that even demons scorn him (especially his transformation).
In one Rikti War Zone/Vanguard arc of City of Heroes, rival organization Longbow becomes full-on Hero Antagonists. Not to mention sister game City of Villains, where Longbow is just one such group.
The Queen Fay and the Elves of the Everlight Sanctuary in Overlord II, even though the Elves are, for the most part, whiny hippies concerned mostly with protecting cute and furry creatures. Eventually, while sacrificing her energy to help the Overlord defeat The Empire, she is corrupted by his magic and becomes a Fallen Hero who decides that Evil Feels Good.
Persona 4 has a subversion with Taro Namatame, who started kidnapping people after the death of Saki Konishi due to being tricked into believing that TV World was a shelter from the true killer, not knowing that all the characters were saved due to the efforts of the Main Character and his friends. The player can either punish him by tossing him into the TV and letting him get slaughtered by Shadows, or hear him out, where they will learn his side of the story, and he, in turn, will understand what he's done and willingly accepting the consequences.
The Metal Gear series is so full of lies and deceptions (and lots of RetCons very well disguised as such) that you can never really tell who is on which side, or even which sides there are. The prime example would be The Boss in MGS3 whose heroic identity is only revealed after being killed by the protagonist.
In Touhou Project 12: Undefined Fantastic Object, the ancient mage the antagonists were trying to unseal turns out to be a Buddhist monk seeking to bring peace and harmony to Youkai. And she still fights you as the final boss.
Technically, the entire plot of Touhou 10: Mountain of Faith counts. Sanae didn't know the Hakurei Shrine was key to Gensokyo's survival; she saw competition for the faith her gods needed to survive, from a Shrine Maiden who wasn't even protecting humanity from the youkai. So she tried to shut down the Hakurei Shrine, and got her ass (and her gods') kicked by Reimu (or Marisa).
Also in Touhou 8: Imperishable Night, the Stage 4 boss is either Reimu or Marisa, the two standard protagonists, who will blame you for the current incident and attempt to stop you.
Similarly, in both of the Touhou Project fighting games, almost every character ends up fighting either Reimu or Marisa at some point in their story mode.
Perhaps the most blatant example is the portrayal of the Watatsuki sisters, Toyohime and Yorihime, from the Spin-Off manga Silent Sinner in Blue. Technically they're just trying to protect their home from invaders, and Reimu even implicitly threatens to kill everyone on the moon at one point to make Yorihime take the fight seriously, But because of the way the narrative is presented along with their Fantastic Racism, many readers came away thinking them as villains.
Debatably the UED in Brood War; Informations in expanted materials suggested they actually are a dictatorial regime, but the army that was featured in the game was fairly sympathetic.
General Warfield in StarCraft II, in stark contrast with his predecessor Edmund Duke. The litterally only reason Warfield is featured as an antagonist in some missions is because he is working for ArcturusMengsk. Other than that, he puts The Men First, is concerned about protecting the population of the Dominion and is remarquably brave. In fact, while he initially isn't happy when Prince Valerian asks him to collaborate with Jim Raynor, they get along quite well after getting to know each other. His death screamAlas, Poor Villain.
Some parts of the campaign in Warcraft III and its expansion have the player control a villainous army, making the enemy army a Hero Antagonist (except the Blackrock orcs, who are pretty evil themselves).
Araman from Neverwinter Nights 2: Mask of the Betrayer. From his point of view, unless the protagonist can be stopped somehow, the world will end.
Okku is this as well, for pretty much the same reason. However, if you decide to spare him after the final fight against him, he'll decide to help you.
Not to mention Master Eraqus. The characters weren't the only ones shedding Manly Tears when that happened.
Riku serves as one in Days, where the story is told from the perspective of a Punch Clock Villain working for the bad guys.
In Sin And Punishment Star Successor, The Nebulox are fighting against Isa and Kachi to help the humans of Earth-5. Also, from their perspective, Kachi is a major danger to their entire civilization - she was originally sent to Inner Space to recon Earth-4 for attack, but lost her memory.
Axel Almer in Super Robot Wars Original Generation gets shades of this in the enhanced remake, becoming a Noble Demon whose greatest concern is to defeat a psychopathic monstrous man (Beowulf) responsible for numerous atrocities in his (Axel's) home world. This is even moreso in The Anime of the Game, where said psychopathic monstrous man's first scene involve crossing the Moral Event Horizon. Then, in the opening credits, Axel fights off the main character (Kyosuke), under justification that he won't let another Beowulf be created from Kyosuke. By the time of the Gaiden Game, he drops the 'Antagonist' part while keeping the same goal (growing an 'Anti' in the front instead due to not being officially in the protagonist team).
Ash from Atelier Iris 3 simply wants to use the Escalario to stop Uroborus from awakening. To do this, he tries to kill Edge and Nell, and kidnap Iris, the only person able to use the Escalario.
Saladin, the captain of the guard at the Castle of the Crown in Kings Quest VI, is perhaps the noblest of all the characters in the game. He has an antagonistic role only because he has been deceived by Alhazred and has a strong sense of duty regarding his job, and he does eventually wise up.
Alakazam and his team in Red/Blue Rescue Team.When the protagonist and teamate end up being tossed into exile, Alakazam and his team are the leaders of the hunt for the protagonist's head.
And Palkia from the sequel, who thinks that the hero is threatening to destroy the universe. However, it turns out that he was tricked: Darkrai was the one threatening to destroy everything, and he actually made it look like it was the hero's fault.
In the first Max Payne, Lt. Jim Bravura and the rest of the NYPD. In the 2nd game, Bravura becomes Da Chief.
The freeware indie game Akuji the Demon has the final boss being the hero who defeated and banished you into the dungeon.
Wiegraf is one of these during the prologue of Final Fantasy Tactics and remains so to a lesser extent, later in the story. He starts out as a Holy Knight fighting against the aristocracy for very justifiable reasons. His only really even vaguely selfish or villainous actions are his attempts to take revenge on Ramza for killing his sister, but Wiegraf also doesn't know that Ramza tried to avoid killing her. Wiegraf later becomes a Fallen Hero, however, as revenge drives him off the slippery slope.
Battle for Wesnoth features campaigns like Descent to Darkness where many antagonists are heroes trying to defeat the necromancers.
Both the NCR and Mr House in Fallout New Vegas if you support Caesar's Legion. The Brotherhood of Steel becomes one in Fallout 3 if you destroy the Citadel. Of course, since this is a series where you can nuke entire cities for kicks, pretty much any decent individual in the wasteland can become one if they get on the wrong side of the player.
Fallout 3 also has the Regulators who will hunt down the player if s/he has Evil Karma.
The censors in Psychonauts are mental antibodies. They're supposed to stamp out foreign influences. Like normal antibodies, they can't really distinguish things except as "native" and "foreign", even if "foreign" is a friendly psychic.
The Knights Templar in Immortal Souls are definitely good guys, as the only group actually devoted to actively fighting the "shadow creatures", which are almost all malevolent and/or mindless and devoted to harming humanity. But since they have a hard time accepting the "almost" in the "almost all"—and their leader is a major Good Is Not Nice jerkass to boot—that brings them into constant conflict with the two good vampires that are the main protagonists.
White Knight Leo from Lunar 2, in the early-going.
Unlike the original film TRON, security programs in Tron 2.0 are not servants of the evil MCP. Here, they're simply doing their job of protecting the system from The Virus. Unfortunately, Kernel, the chief security program, thinks you are the cause of the infection and tries to hunt you down, forcing you to fight security programs.
Berk, who appears at first as Gwynn's weird and annoying new boyfriend, but then, in the chapter "K'Z'K", tries to assassinate several main characters — because he's been sent from the future to stop them from causing The End of the World as We Know It by summoning the demon K'Z'K.
Miko Miyazaki of The Order of the Stick. A Lawful Good paladin that takes 'lawful' to ridiculous levels, she becomes convinced that the Order of the Stick are evil and tries to destroy them. She is so sure of herself and her own importance that she winds up causing a lot of damage, all the while thinking she was doing good. (Also, many characters and readers found her just plain annoying). That being said, her initial reason for pursuing the Order was that they were responsible (albeit unintentionally) for weakening the fabric of reality, and she came across a lot of evidence to suggest they were evil and dangerous (Roy and Elan landed on the Flumphs, Nale and Thog, their evil lookalikes, abused a dwarf, Belkar unnecessarily killed 3 barbarians as part of his initiation, and the weasel got chucked into the gaping mouths of a troll...ogre...large green brute thingie)
She eventually manages to work her delusion around to the point that she commits an unquestionably evil act (killing a man who, while by no means pure as the driven snow, really was acting for the greater good and certainly was innocent of the crime for which he was killed), falls, and still manages to convince herself that she's the gods' favored warrior and that this is some kind of test she has to overcome. Not that this means much to Miko now, seeing as she's dead and all. She remains erroneously and stubbornly convinced of the justness of her actions, and only has vague realizations when the ghost of the founder of her order explained to her in detail how she screwed up during her final moments.
In Start of Darkness, the members of the Order of the Scribble, most notably Durokan and Lirian, serve this to Xykon and Redcloak.
Othar Tryggvasen (Gentleman Adventurer!) of Girl Genius. A very interesting example, in that his stated goal of killing all the world's Sparks, ending finally with him committing suicide, appears to place him squarely in the realm of being a Villain with Good Publicity. It is only when one looks at how nearly every Spark he has ever encountered has acted, killing dozens to thousands of innocent people, either deliberately or as an accidental consequence of their mad inventions, to the point of having already severely depopulated the entire continent of Europe (as documented in his twitter account on the Girl Genius website), that it becomes clear that he may be a legitimate hero whose actions are fully justified. Indeed, the heroine of the story, whom he previously tried to kill when she was completely innocent has since killed hundreds of innocent people after being possessed by the spirit of another spark, and in one possible future timeline, his failure to complete his self-appointed mission results in the apparent eradication of human life in Western Europe, apparently within a few years of the main storyline.
Note that Othar clearly could have killed DuMedd (himself a spark) had he wanted to, but never did anything (harmful) to him or even brought up his "kill-all-sparks" agenda upon learning he was not only a fan of Othar himself but also Agatha's cousin. His goals may not be so extreme as he claimed when he was in The Madness Place.
On the other hand, his twitter has him killing a college student and her father (Because she was a spark and he said that the worst thing that could happen to a parent is their child to die before he did), derailing a train and becoming a Cop Killer.
Klaus Wulfenbach is an even straighter example. He's almost the Only Sane Man in Europe, which means that he's got to play whack-a-mole with every crazed Spark or creation that gets loose. And given Agatha's family history, he's got every reason to want to keep her locked down until she can be proven safe. Of course, as Agatha is the protagonist, she isn't about to tamely sit down and let him hold her.
It's even worse in that he is half-rightly convinced that Agatha could be the Biggest Bad of all time — the spark that destroyed most of Europe while he was removed from the picture decades ago and who may have the secrets of time travel on top of a host of other horrifying technologies. If he's right, he has to destroy her to save the world. Unfortunately, he doesn't have the full picture, and the pieces he knows look really bad for Agatha.
Everybody has an "Evil Twin", right? Well, these guys see our Weatherlight crew as theirevil twins and act accordingly. They're not villains, per se, but everybody hates them.
Last Res0rt features Jason Spades, a hero on his home planet of Fenirel who happens to want to viciously kill Daisy to the exclusion of everything else, even if 'everything else' is something like getting the rest of the crew (including himself!) off an enemy ship alive.
In the Whateley Universe, the Reverend Darren England, protector of the planet from demonic threats for decades. He's now willing to deal with The Syndicate if it means the death of The Kellith, the descendant of a Great Old One, before The Kellith can destroy all life on earth. The only problem is that The Kellith is Carmilla, who is an Anti-Hero protagonist and is trying to go straight.
The Insurrectionists/Charon Industries are this in the prequel segments of Red vs. Blue, in opposition to the Freelancers, who are Villain Protagonists at that point.
Though, when we see the leader in Season 7, they've killed the excavation team at Sandtrap, and are trying to get their hands on Ancient Alien weaponry, so they might not actually be the good guys, just a different group opposed to Freelancer.
Dib from Invader Zim, an eleven-year-old paranormal investigator trying to prevent the alien Zim from taking over the world. However, Invader Zim has numerous Villain Episodes where Dib is the main character, making him the protagonist (and usually casting Zim as the antagonist) a good portion of the time.
Dib is really closer to the Deuteragonist. He and Zim team up almost as often as they fight, and a fair number of episodes are about Dib dealing with other stuff while Zim makes only a cursory appearance.
The Road Runner of Looney Tunes fame is one of the most iconic Hero Antagonist of Western Animation; the shorts granted little character to the bird outside his fast speed and his trademark "Beep Beep", and all sympathetic spotlight was deliberately kept on its predator, Wile E. Coyote.
Other Looney Tunes protagonists such as Bugs and Speedy occasionally leaned into this trope as well, many of their respective shorts focusing more on the blundering of their foes.
In "Fresh Hare", Elmer Fudd is only chasing Bugs because he is a mountie and Bugs has been charged with crimes. In "Big House Bunny," Bugs escapes hunters but ends up tunneling into a prison. Yosemite Sam is the guard and only goes after Bugs because he believes Bugs is an escaped prisoner.
In some Daffy Duck cartoons, Porky Pig is an authority figure such as a police officer trying persuing Daffy for his antics. While the nature of some of his "crimes" can be rather disproportionate (in "Daffy Doodles" for example he becomes Public Enemy Number One for painting mustaches on advertisement posters) Porky is clearly the higher moral ground.
The Yankee Doodle Pigeon of Dastardly and Muttley in Their Flying Machines was implied to be of heroic alliance, delivering important messages to squadrons. However, his role rarely exceeded outside blowing his patriotic trumpet and giving bewildered glances to the Vulture Squadron's blundering attempts to "Stop That Pigeon".
Ranger Smith from Yogi Bear. All he's trying to do is keep Yogi and Boo Boo from stealing food from the campers at Jellystone Park. A few cartoons show that he even cares for them and gets upset if he thinks they're in trouble.
Xander Crews from Frisky Dingo, also known as the superhero Awesome X. He's also one of the biggest dicks in a show made almost entirely of dicks, sometimes even more than Killface himself (who kills one of his PR reps in the first episode and then uses the guy's remains as a ventriloquist dummy in front of his twin brother.)
The Centauri Empire officers in the Teen Titans episode Sisters only attacked the Titans due to misunderstanding that they thought Starfire was committing a thievery on their solar system when in truth, Blackfire was the one doing it and framed Starfire for it. Once that was cleared off, they successfully capture Blackfire and then never threatened the Earth anymore, therefore they're pretty much their planet's good police doing their job. Their conversation also kinda imply this:
Officer: In the name of the Centauri Empire, you are all under arrest!