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* Tres Magia in ''Manga/GushingOverMagicalGirls'' would be the protagonist team in any other traditional Magical Girl manga and anime, but that honor goes to [[VillainProtagonist Enormeeta]], the villainous organization they oppose, and their [[AscendedFanboy devout fangirl]] Utena Hiiragi found herself fighting for.
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* Tres Magia in ''Manga/GushingOverMagicalGirls'' ''Gushing Over Magical Girls'' would be the protagonist team in any other traditional Magical Girl manga and anime, but that honor goes to [[VillainProtagonist Enormeeta]], the villainous organization they oppose, and their [[AscendedFanboy devout fangirl]] Utena Hiiragi found herself fighting for.
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* Tres Magia in ''Manga/GushingOverMagicalGirls'' would be the protagonist team in any other traditional Magical Girl manga and anime, but that honor goes to [[VillainProtagonist Enormeeta]], the villainous organization they oppose, and their [[AscendedFanboy devout fangirl]] Utena Hiiragi found herself fighting for.
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* Ryuhou from ''Anime/{{Scryed}}'' is less evil and more concerned with the welfare of most people than the JerkWithAHeartOfGold protagonist, Kazuma. And 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.
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* Ryuhou from ''Anime/{{Scryed}}'' ''Anime/SCryEd'' is less evil and more concerned with the welfare of most people than the JerkWithAHeartOfGold protagonist, Kazuma. And 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.
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* ''Anime/AfroSamurai'': Due to Afro's AntiHero bordering VillainProtagonist status, Shichigoro from ''Resurrection'' fits here.
* [[spoiler:Angel, a.k.a. Tachibana Kanade]], in ''Anime/AngelBeats''. The whole thing was a case of PoorCommunicationKills, and when they actually sit down and ''talk'' to each other they find they have no reason to fight anymore.
* ''Manga/{{Bleach}}'': The entire Seireitei [[spoiler:(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.
* Officer Kirihara of ''Anime/DarkerThanBlack''. She is good and hunting the protagonist for crimes he actually committed [[spoiler: but also [[UnwittingPawn being misled]] by her [[ConspiracyRedemption evil superiors]]]]
* ''Manga/DeathNote'':
** L, the [[GreatDetective world’s greatest detective]], is a Pragmatic Hero Antagonist dedicated to catching the SerialKillerKiller Kira (aka the VillainProtagonist Light Yagami), [[spoiler:as are his successors.]]
** Matsuda is a classic IdiotHero -- a slightly impulsive but very well-meaning everyman who's ultimately devoted to his TrueCompanions in their quest to catch Kira -- too bad one of his aforementioned friends is secretly BigBad Light Yagami, AKA Kira.
** Soichiro Yagami is a police chief who also wants to catch Kira (not knowing the perp is his own son), and he is described by the author as the only one-hundred-percent good character. However neither he nor Matsuda are Light's direct antagonist as such, while L [[spoiler:and Near]] are.
* ''Anime/DragonBallSuper'':
** In the Universe Survival Saga, [[TopGod Zen-Oh]] decided to hold a battle royale-style martial arts tournament, but declared that any universe that's eliminated will be erased from existence. Thus, everyone is literally fighting for survival, not just for themselves but for countless lives. Universe 11 and 2's teams are outright superheroes (the former a riff on Franchise/SuperSentai and the latter consisting of a trio of {{Magical Girl}}s and their supporters) and most of Universe 6's team make friends with Goku and company in previous arcs. Some of them antagonize Goku because they blame him for what's happening[[note]]Goku suggested the tournament, but Zen-O decided to use it as an excuse to get rid of some of the universes. Several observers remark that since the tournament at least spares one universe (whereas before Zen-O was going to erase all eight no questions asked), people should be ''thanking'' Goku for giving them a fighting chance.[[/note]]; [[BloodKnight he's perfectly willing to be labeled the bad guy if it means people will fight him with everything they've got]]. In fact, he willingly admits that Universe 11's Pride Troopers have one up on him because they fight ForGreatJustice while he's just a martial artist looking for a challenge.
** The manga version of [[WorldsStrongestMan Jiren]], one of the aforementioned Pride Troopers, is probably the best example in the tournament: he's a selfless champion of justice who has saved his own universe countless times and is known as a great hero in it for his deeds. He devotes all his time to running around the universe, protecting civilians and righting wrongs, and won't even kill villains. He's a much more straightforwardly heroic character than anyone in the main cast, who are mostly martial artists who do very few heroic things unless essentially forced to. He's only against the main characters because of the circumstances of the tournament, and he initially wasn't even going to compete, saying that he'd rather be erased than take part in such an immoral display (Goku, on the other hand, didn't even blink at the idea). His anime self would count too if not for a huge dose of AdaptationalVillainy.
** The movie ''Anime/DragonBallSuperBroly'' actually turns the series main characters Son Goku and Vegeta into this, albeit of the AntiHero variety, due to the titular [[AntiVillain Broly]] [[VillainProtagonist being the main character]]. Broly is not a villainous character, he is tragically a good person who is blindly obedient to his [[AbusiveParents cruel father Paragus]] and the victim of [[ManipulativeBastard Frieza's]] manipulations. Both Broly and Paragus are recruited by Frieza, who wants to test Broly's power by sending him to Earth to fight Goku and Vegeta. This naturally puts them in conflict, as as far Vegeta knows, Broly is simply an evil warrior working for Frieza. Goku manages to deduce that Broly isn't evil and while he [[BloodKnight enjoys fighting him]], he doesn't want to kill him but Broly's out of control power leaves him with little choice.
* ''Manga/ElfenLied'':
** Shirakawa, initially a cold GirlFriday to Kurama, [[spoiler: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 hate Lucy, and they pilot the vector craft to attack the facility and kill any and all Diclonii, and retrieve the cure to the disease, which has just been used to infect everyone in the world. They still have no problems with lying and shooting unarmed people as long as they complete their task.
** The Agent is initially just a replacement field operative after Bando and The Unknown man were indisposed. [[spoiler: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.]]
%%* ''Manga/FairyTail'':
%%** The magic council, especially Doranbolt and Lahal.
%%** ''Every competing guild'' in the TournamentArc save, Raven Taileven, including [[GoodIsNotNice Sabertooth]]. Then came Chapter 281, it shows that Sabertooth isn't so good after all.
* In ''Anime/GhostInTheShellStandAloneComplex'', there are the soldiers who [[spoiler:storm and arrest the members of Section 9]] -- they're very much aware of what they're doing, so they're not InspectorJavert, but they are approved by the city and they limit the use of lethal force.
* ''Manga/{{Hellsing}}'': Father Alexander Anderson is a NobleDemon and SociopathicHero, sure, but he specifically targets vampires and heathens and attempts to keep civilians out of the line of fire, even forfeiting a chance to battle [[TheRival Alucard]] because of there being too many innocents in the museum. He despises rapists as well, and is willing to escort Integra back to Hellsing Manor "to protect her maiden virtue", which is quite telling after VillainProtagonist Alucard's [[FanDisservice encounter with Rip Van Winkle]]. Vatican Section XIII, the Iscariot Organization to which Anderson belongs meanwhile, [[spoiler:goes well off the deep end in the manga and OVA by waging another crusade on ''both'' [[ThoseWackyNazis Millennium]] and all of Protestant England, swinging them into literal KnightTemplar territory]]. This highlights Anderson's own moral compass because [[spoiler:he assists in killing his own boss/surrogate son for his crimes]].
* In ''Anime/TheLegendOfHeroesTrailsOfColdSteelNorthernWar'', the protagonist of the ''Cold Steel'' saga from the ''VideoGame/TrailsSeries'' and a heroic individual, [[VideoGame/TheLegendOfHeroesTrailsOfColdSteel Rean Schwarzer]], is this trope as the main point of view in the anime is from the cast of North Ambria. From their perspective, Rean is the biggest threat of the country thanks to his HumongousMecha and if he's not stopped, North Ambria will ultimately get conquered.
* [[SympatheticInspectorAntagonist Inspector Zenigata]] from ''Characters/LupinIII''. Our main character is a criminal, and Zenigata is attempting to bring him in for his crimes. [[FailureIsTheOnlyOption Key word being attempting]].
* ''Anime/MagicalGirlLyricalNanohaAs'':
** The Wolkenritter. So here we have a group of "villains" whose malicious goal for filling up the ArtifactOfDoom 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. [[spoiler:Either the Book of Darkness would have killed the girl and reincarnated elsewhere, or Admiral Graham would have frozen them both forever.]]
** [[spoiler:Admiral Graham]] himself. He's a WellIntentionedExtremist who wanted to stop the Book of Darkness forever. Most previous masters of the Book of Darkness abuses it for their evil ambitions and they used the Wolkenritter as killers.
* ''Franchise/{{Gundam}}'':
** Zechs Merquise from ''Anime/MobileSuitGundamWing''; 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 [[RebelliousPrincess Relena]], the show's female lead, is going for. The major difference is that Zechs is a WellIntentionedExtremist more than willing to hold the VillainBall in order to scare the planet towards peace -- and his personal pride keeps drawing him into battles with protagonist [[TheStoic Heero]].
** ''Anime/MobileSuitGundamSEEDDestiny'' is complicated (in this and many other areas) due to events that some fans consider signs of [[CreatorsPet creator favoritism]]. Both Shinn Asuka (the show's initial protagonist) and Kira Yamato (protagonist of [[Anime/MobileSuitGundamSEED the previous series]]) want the same thing: to end the bloody, destructive war and protect the innocents caught in the crossfire. However, they're on different sides, have different methods, and eventually [[ItsPersonal a few bodies between them]] so they come to blows all throughout the series. [[spoiler:In the end, however, [[DecoyProtagonist Shinn]] grabs the VillainBall ''hard'' in [[RevengeBeforeReason his misguided and vengeful desire to destroy Orb]] and help [[BigBad Gilbert Durandal]] bring his [[WellIntentionedExtremist Destiny Plan]] to fruition, leading Kira -- and Shinn's failed mentor, Athrun -- to stop him. Therefore, Shinn becomes a VillainProtagonist as Kira reassumes the role of TheHero (or if you prefer, Athrun being the true hero of ''Destiny'').]]
** ''Anime/MobileSuitGundam00'' has multiple examples:
*** [[ColonelBadass Col. Sergei Smirnov]], a.k.a. the "Wild Bear of Russia", is, far and away, the most sympathetic out of all of Celestial Being's antagonists in the first season. A ReasonableAuthorityFigure in the Human Reform League who believes in upholding the law, flawed as it may be, against an organization of terrorists (albeit, [[WellIntentionedExtremist well intentioned ones]]), and helped give the first season its GreyAndGrayMorality.
*** [[AcePilot Graham Aker]] of the Union and later Earth Sphere Federation, with his sportsman-like qualities or rather Samurai-like hence his nickname "Mr. Bushido".
*** [[TheStrategist Kati Mannequin]] of AEU considers Celestial Being's commander Sumeragi to be a WorthyOpponent even if Kati [[spoiler:initially]] views Sumeragi's goals to be unfeasible and too idealistic. [[spoiler:not too surprising given how Sumeragi used to serve alongside Kati in the AEU]].
** Since ''Anime/GundamBuildFighters'' is all about people building custom Gunpla[[note]]''Gundam'' model kits[[/note]] and battling them using a special machine, almost every single character is a ''Gundam'' fan and a modeller, giving them a few common interests right off the bat. Even the fact that they're participating in a tournament doesn't stop the characters from getting along, and in both this series and [[Anime/GundamBuildFightersTry its sequel]] the main characters start off as or end up befriending almost every opponent they face, including having a strong {{Friendly Rival}}ry with their primary opponents. The rare few exceptions are characters who fit the OpposingSportsTeam mold like the Renato brothers from the original series, or those who are just straight-up {{Jerkass}}es like Saga Adou from ''Try''.
* ''Manga/{{Monster}}'': During Martin's flashback, Tenma and Martin are both trying to save Eva, but neither one knows or trusts the other. They're [[HeroOfAnotherStory heroes of their own stories]], Tenma not sure Martin isn't trying to kill Eva, and Martin believing he's protecting Eva from Tenma.
* The court in ''Literature/MoribitoGuardianOfTheSpirit''. 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. [[spoiler:They learn otherwise, which ends up aligning them with the heroes instead.]]
* ''Manga/NegimaMagisterNegiMagi'':
** [[spoiler:Chao Lingshen]]. The only reason the main character opposes her in the end is, basically, to avoid the CoolAndUnusualPunishment he would incur from the authorities if he didn't. And because she absolutely refuses to explain her actions, despite the fact that he'd agree with her if she did. It turns out [[XanatosGambit winning was actually her Plan B. Plan A was for Negi to defeat her, proving he could handle the rest without her help]].
** [[spoiler:Cosmo Entelechia]], though somewhat more dickish about it than necessary. Ultimate plan? [[spoiler:Save over a billion lives.]]
* ''Manga/OnePiece'':
** A few of the Marine Officers the main characters have to face are genuinely good guys who actually want to protect the public and don't view [[MoralEventHorizon civilians]] and their own soldiers as being [[WeHaveReserves completely expendable]]. Notable examples are Smoker and Tashigi (who have practically achieved FriendlyEnemy status with the Straw Hats), T-Bone (AFatherToHisMen), Coby (Luffy's old friend and rising Marine equal), Garp (Luffy's grandfather), Kuzan (a.k.a. Aokiji), and Issho (a.k.a. Fujitora, one of the new guys).
** One filler arc included the presence of a rational, normal [[AFatherToHisMen Marine captain]], who had no strange abilities or quirks, but was led by some crazy, immensely fat admiral and his equally stupid lieutenant, who were on par with all the early, lighter ''One Piece'' villains.
** Commander Jonathan of the G8 filler arc. 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.
** Magellan and Hannyabal, the chief warden and vice-chief warden of Impel Down. While the latter is a bit promotion-happy, he is genuine in doing his job to protect the outside world from the criminals in Impel Down, even saying this in his fight with Luffy, due to the latter inadvertently starting a prison breakout.
** [[spoiler:Former]] Fleet Admiral Sengoku has done some... questionable things in the past (Ohara), but there is no question that he only does those things for what he feels is for the good of the world. [[spoiler:And some part of him has always been [[TheChainsOfCommanding suffering]] for it. He finally retired when the World Government decided to cover up the breakout of several Level Six Impel Down prisoners in order to save their reputation, instead of sending out warnings and wanted posters like ''he'' wanted to do.]]
** The Galley-La Shipwrights start out as this in the Water Seven arc. After Nico Robin participates in an assassination attempt on Iceberg alongside [=CP9=], the shipwrights are convinced that the Straw Hats are responsible, and try to hunt them down. After realizing that they had been deceived, they fight alongside the Straw Hats and Franky Family in the raid on Enies Lobby.
* [[spoiler:[[WellIntentionedExtremist Oswald/Glen Baskerville]]]] of ''Manga/PandoraHearts'' only wants to reverse the effects of what [[ItsAllMyFault he believes]] his own naivety caused one hundred years ago. By going through with his plan he would [[spoiler:erase a good many characters from the timeline but would also prevent the deaths of countless innocents]]. Unsurprisingly, GreyAndGrayMorality abounds.
* ''Manga/PhantomThiefJeanne'' has Miyako, her best friend and pursuer, and [[spoiler:Chiaki/Sinbad, who tries to stop her from helping the Devil because he is working for God all along]].
* Ryuhou from ''Anime/{{Scryed}}'' is less evil and more concerned with the welfare of most people than the JerkWithAHeartOfGold protagonist, Kazuma. And 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.
* By the end of ''Literature/ShakuganNoShana'', [[spoiler:Yuji Sakai with Snake of the Festival get to save the world and make the Flame Haze the bad guys without them knowing it]].
* The aliens in ''Anime/TokyoMewMew'' are trying to kill humans and take the planet back, as their ancestors used to live on Earth, but at the end of the day, they are trying to save their loved ones as much as the mews (the anime itself lampshades this).
* Ultra Magnus (God Magnus) in ''Anime/TransformersRobotsInDisguise''/''Car Robots''. He's arrogant and bitter about Optimus being chosen to carry the Matrix instead of him, but he's no friend of the Predacons or Decepticons, and at least once rebuffs Scourge/Black Convoy outright when the latter thinks that just because he's Optimus' rival that it somehow makes him a bad guy. He just really, really wants the Matrix, and isn't above roughing up Optimus to get it, making him a third-party antagonist for much of his early appearances. In spite of his superiority complex, he's also not above saving humans, either, meaning that while Magnus comes off as a dick, he's still got a good spark somewhere beneath all that ego.
* Team Unicorn and Team Ragnarok of ''Anime/YuGiOh5Ds'' are {{Opposing Sports Team}}s competing against the protagonists, so the protagonists have to defeat them even though there's nothing evil or villainous about them -- they believe in ThePowerOfFriendship just like the heroes, they care about and protect each other, they fight fair, and they don't want to hurt anyone. If they weren't competing against the characters the story had been long been following already, they would be heroes.
----
* [[spoiler:Angel, a.k.a. Tachibana Kanade]], in ''Anime/AngelBeats''. The whole thing was a case of PoorCommunicationKills, and when they actually sit down and ''talk'' to each other they find they have no reason to fight anymore.
* ''Manga/{{Bleach}}'': The entire Seireitei [[spoiler:(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.
* Officer Kirihara of ''Anime/DarkerThanBlack''. She is good and hunting the protagonist for crimes he actually committed [[spoiler: but also [[UnwittingPawn being misled]] by her [[ConspiracyRedemption evil superiors]]]]
* ''Manga/DeathNote'':
** L, the [[GreatDetective world’s greatest detective]], is a Pragmatic Hero Antagonist dedicated to catching the SerialKillerKiller Kira (aka the VillainProtagonist Light Yagami), [[spoiler:as are his successors.]]
** Matsuda is a classic IdiotHero -- a slightly impulsive but very well-meaning everyman who's ultimately devoted to his TrueCompanions in their quest to catch Kira -- too bad one of his aforementioned friends is secretly BigBad Light Yagami, AKA Kira.
** Soichiro Yagami is a police chief who also wants to catch Kira (not knowing the perp is his own son), and he is described by the author as the only one-hundred-percent good character. However neither he nor Matsuda are Light's direct antagonist as such, while L [[spoiler:and Near]] are.
* ''Anime/DragonBallSuper'':
** In the Universe Survival Saga, [[TopGod Zen-Oh]] decided to hold a battle royale-style martial arts tournament, but declared that any universe that's eliminated will be erased from existence. Thus, everyone is literally fighting for survival, not just for themselves but for countless lives. Universe 11 and 2's teams are outright superheroes (the former a riff on Franchise/SuperSentai and the latter consisting of a trio of {{Magical Girl}}s and their supporters) and most of Universe 6's team make friends with Goku and company in previous arcs. Some of them antagonize Goku because they blame him for what's happening[[note]]Goku suggested the tournament, but Zen-O decided to use it as an excuse to get rid of some of the universes. Several observers remark that since the tournament at least spares one universe (whereas before Zen-O was going to erase all eight no questions asked), people should be ''thanking'' Goku for giving them a fighting chance.[[/note]]; [[BloodKnight he's perfectly willing to be labeled the bad guy if it means people will fight him with everything they've got]]. In fact, he willingly admits that Universe 11's Pride Troopers have one up on him because they fight ForGreatJustice while he's just a martial artist looking for a challenge.
** The manga version of [[WorldsStrongestMan Jiren]], one of the aforementioned Pride Troopers, is probably the best example in the tournament: he's a selfless champion of justice who has saved his own universe countless times and is known as a great hero in it for his deeds. He devotes all his time to running around the universe, protecting civilians and righting wrongs, and won't even kill villains. He's a much more straightforwardly heroic character than anyone in the main cast, who are mostly martial artists who do very few heroic things unless essentially forced to. He's only against the main characters because of the circumstances of the tournament, and he initially wasn't even going to compete, saying that he'd rather be erased than take part in such an immoral display (Goku, on the other hand, didn't even blink at the idea). His anime self would count too if not for a huge dose of AdaptationalVillainy.
** The movie ''Anime/DragonBallSuperBroly'' actually turns the series main characters Son Goku and Vegeta into this, albeit of the AntiHero variety, due to the titular [[AntiVillain Broly]] [[VillainProtagonist being the main character]]. Broly is not a villainous character, he is tragically a good person who is blindly obedient to his [[AbusiveParents cruel father Paragus]] and the victim of [[ManipulativeBastard Frieza's]] manipulations. Both Broly and Paragus are recruited by Frieza, who wants to test Broly's power by sending him to Earth to fight Goku and Vegeta. This naturally puts them in conflict, as as far Vegeta knows, Broly is simply an evil warrior working for Frieza. Goku manages to deduce that Broly isn't evil and while he [[BloodKnight enjoys fighting him]], he doesn't want to kill him but Broly's out of control power leaves him with little choice.
* ''Manga/ElfenLied'':
** Shirakawa, initially a cold GirlFriday to Kurama, [[spoiler: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 hate Lucy, and they pilot the vector craft to attack the facility and kill any and all Diclonii, and retrieve the cure to the disease, which has just been used to infect everyone in the world. They still have no problems with lying and shooting unarmed people as long as they complete their task.
** The Agent is initially just a replacement field operative after Bando and The Unknown man were indisposed. [[spoiler: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.]]
%%* ''Manga/FairyTail'':
%%** The magic council, especially Doranbolt and Lahal.
%%** ''Every competing guild'' in the TournamentArc save, Raven Taileven, including [[GoodIsNotNice Sabertooth]]. Then came Chapter 281, it shows that Sabertooth isn't so good after all.
* In ''Anime/GhostInTheShellStandAloneComplex'', there are the soldiers who [[spoiler:storm and arrest the members of Section 9]] -- they're very much aware of what they're doing, so they're not InspectorJavert, but they are approved by the city and they limit the use of lethal force.
* ''Manga/{{Hellsing}}'': Father Alexander Anderson is a NobleDemon and SociopathicHero, sure, but he specifically targets vampires and heathens and attempts to keep civilians out of the line of fire, even forfeiting a chance to battle [[TheRival Alucard]] because of there being too many innocents in the museum. He despises rapists as well, and is willing to escort Integra back to Hellsing Manor "to protect her maiden virtue", which is quite telling after VillainProtagonist Alucard's [[FanDisservice encounter with Rip Van Winkle]]. Vatican Section XIII, the Iscariot Organization to which Anderson belongs meanwhile, [[spoiler:goes well off the deep end in the manga and OVA by waging another crusade on ''both'' [[ThoseWackyNazis Millennium]] and all of Protestant England, swinging them into literal KnightTemplar territory]]. This highlights Anderson's own moral compass because [[spoiler:he assists in killing his own boss/surrogate son for his crimes]].
* In ''Anime/TheLegendOfHeroesTrailsOfColdSteelNorthernWar'', the protagonist of the ''Cold Steel'' saga from the ''VideoGame/TrailsSeries'' and a heroic individual, [[VideoGame/TheLegendOfHeroesTrailsOfColdSteel Rean Schwarzer]], is this trope as the main point of view in the anime is from the cast of North Ambria. From their perspective, Rean is the biggest threat of the country thanks to his HumongousMecha and if he's not stopped, North Ambria will ultimately get conquered.
* [[SympatheticInspectorAntagonist Inspector Zenigata]] from ''Characters/LupinIII''. Our main character is a criminal, and Zenigata is attempting to bring him in for his crimes. [[FailureIsTheOnlyOption Key word being attempting]].
* ''Anime/MagicalGirlLyricalNanohaAs'':
** The Wolkenritter. So here we have a group of "villains" whose malicious goal for filling up the ArtifactOfDoom 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. [[spoiler:Either the Book of Darkness would have killed the girl and reincarnated elsewhere, or Admiral Graham would have frozen them both forever.]]
** [[spoiler:Admiral Graham]] himself. He's a WellIntentionedExtremist who wanted to stop the Book of Darkness forever. Most previous masters of the Book of Darkness abuses it for their evil ambitions and they used the Wolkenritter as killers.
* ''Franchise/{{Gundam}}'':
** Zechs Merquise from ''Anime/MobileSuitGundamWing''; 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 [[RebelliousPrincess Relena]], the show's female lead, is going for. The major difference is that Zechs is a WellIntentionedExtremist more than willing to hold the VillainBall in order to scare the planet towards peace -- and his personal pride keeps drawing him into battles with protagonist [[TheStoic Heero]].
** ''Anime/MobileSuitGundamSEEDDestiny'' is complicated (in this and many other areas) due to events that some fans consider signs of [[CreatorsPet creator favoritism]]. Both Shinn Asuka (the show's initial protagonist) and Kira Yamato (protagonist of [[Anime/MobileSuitGundamSEED the previous series]]) want the same thing: to end the bloody, destructive war and protect the innocents caught in the crossfire. However, they're on different sides, have different methods, and eventually [[ItsPersonal a few bodies between them]] so they come to blows all throughout the series. [[spoiler:In the end, however, [[DecoyProtagonist Shinn]] grabs the VillainBall ''hard'' in [[RevengeBeforeReason his misguided and vengeful desire to destroy Orb]] and help [[BigBad Gilbert Durandal]] bring his [[WellIntentionedExtremist Destiny Plan]] to fruition, leading Kira -- and Shinn's failed mentor, Athrun -- to stop him. Therefore, Shinn becomes a VillainProtagonist as Kira reassumes the role of TheHero (or if you prefer, Athrun being the true hero of ''Destiny'').]]
** ''Anime/MobileSuitGundam00'' has multiple examples:
*** [[ColonelBadass Col. Sergei Smirnov]], a.k.a. the "Wild Bear of Russia", is, far and away, the most sympathetic out of all of Celestial Being's antagonists in the first season. A ReasonableAuthorityFigure in the Human Reform League who believes in upholding the law, flawed as it may be, against an organization of terrorists (albeit, [[WellIntentionedExtremist well intentioned ones]]), and helped give the first season its GreyAndGrayMorality.
*** [[AcePilot Graham Aker]] of the Union and later Earth Sphere Federation, with his sportsman-like qualities or rather Samurai-like hence his nickname "Mr. Bushido".
*** [[TheStrategist Kati Mannequin]] of AEU considers Celestial Being's commander Sumeragi to be a WorthyOpponent even if Kati [[spoiler:initially]] views Sumeragi's goals to be unfeasible and too idealistic. [[spoiler:not too surprising given how Sumeragi used to serve alongside Kati in the AEU]].
** Since ''Anime/GundamBuildFighters'' is all about people building custom Gunpla[[note]]''Gundam'' model kits[[/note]] and battling them using a special machine, almost every single character is a ''Gundam'' fan and a modeller, giving them a few common interests right off the bat. Even the fact that they're participating in a tournament doesn't stop the characters from getting along, and in both this series and [[Anime/GundamBuildFightersTry its sequel]] the main characters start off as or end up befriending almost every opponent they face, including having a strong {{Friendly Rival}}ry with their primary opponents. The rare few exceptions are characters who fit the OpposingSportsTeam mold like the Renato brothers from the original series, or those who are just straight-up {{Jerkass}}es like Saga Adou from ''Try''.
* ''Manga/{{Monster}}'': During Martin's flashback, Tenma and Martin are both trying to save Eva, but neither one knows or trusts the other. They're [[HeroOfAnotherStory heroes of their own stories]], Tenma not sure Martin isn't trying to kill Eva, and Martin believing he's protecting Eva from Tenma.
* The court in ''Literature/MoribitoGuardianOfTheSpirit''. 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. [[spoiler:They learn otherwise, which ends up aligning them with the heroes instead.]]
* ''Manga/NegimaMagisterNegiMagi'':
** [[spoiler:Chao Lingshen]]. The only reason the main character opposes her in the end is, basically, to avoid the CoolAndUnusualPunishment he would incur from the authorities if he didn't. And because she absolutely refuses to explain her actions, despite the fact that he'd agree with her if she did. It turns out [[XanatosGambit winning was actually her Plan B. Plan A was for Negi to defeat her, proving he could handle the rest without her help]].
** [[spoiler:Cosmo Entelechia]], though somewhat more dickish about it than necessary. Ultimate plan? [[spoiler:Save over a billion lives.]]
* ''Manga/OnePiece'':
** A few of the Marine Officers the main characters have to face are genuinely good guys who actually want to protect the public and don't view [[MoralEventHorizon civilians]] and their own soldiers as being [[WeHaveReserves completely expendable]]. Notable examples are Smoker and Tashigi (who have practically achieved FriendlyEnemy status with the Straw Hats), T-Bone (AFatherToHisMen), Coby (Luffy's old friend and rising Marine equal), Garp (Luffy's grandfather), Kuzan (a.k.a. Aokiji), and Issho (a.k.a. Fujitora, one of the new guys).
** One filler arc included the presence of a rational, normal [[AFatherToHisMen Marine captain]], who had no strange abilities or quirks, but was led by some crazy, immensely fat admiral and his equally stupid lieutenant, who were on par with all the early, lighter ''One Piece'' villains.
** Commander Jonathan of the G8 filler arc. 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.
** Magellan and Hannyabal, the chief warden and vice-chief warden of Impel Down. While the latter is a bit promotion-happy, he is genuine in doing his job to protect the outside world from the criminals in Impel Down, even saying this in his fight with Luffy, due to the latter inadvertently starting a prison breakout.
** [[spoiler:Former]] Fleet Admiral Sengoku has done some... questionable things in the past (Ohara), but there is no question that he only does those things for what he feels is for the good of the world. [[spoiler:And some part of him has always been [[TheChainsOfCommanding suffering]] for it. He finally retired when the World Government decided to cover up the breakout of several Level Six Impel Down prisoners in order to save their reputation, instead of sending out warnings and wanted posters like ''he'' wanted to do.]]
** The Galley-La Shipwrights start out as this in the Water Seven arc. After Nico Robin participates in an assassination attempt on Iceberg alongside [=CP9=], the shipwrights are convinced that the Straw Hats are responsible, and try to hunt them down. After realizing that they had been deceived, they fight alongside the Straw Hats and Franky Family in the raid on Enies Lobby.
* [[spoiler:[[WellIntentionedExtremist Oswald/Glen Baskerville]]]] of ''Manga/PandoraHearts'' only wants to reverse the effects of what [[ItsAllMyFault he believes]] his own naivety caused one hundred years ago. By going through with his plan he would [[spoiler:erase a good many characters from the timeline but would also prevent the deaths of countless innocents]]. Unsurprisingly, GreyAndGrayMorality abounds.
* ''Manga/PhantomThiefJeanne'' has Miyako, her best friend and pursuer, and [[spoiler:Chiaki/Sinbad, who tries to stop her from helping the Devil because he is working for God all along]].
* Ryuhou from ''Anime/{{Scryed}}'' is less evil and more concerned with the welfare of most people than the JerkWithAHeartOfGold protagonist, Kazuma. And 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.
* By the end of ''Literature/ShakuganNoShana'', [[spoiler:Yuji Sakai with Snake of the Festival get to save the world and make the Flame Haze the bad guys without them knowing it]].
* The aliens in ''Anime/TokyoMewMew'' are trying to kill humans and take the planet back, as their ancestors used to live on Earth, but at the end of the day, they are trying to save their loved ones as much as the mews (the anime itself lampshades this).
* Ultra Magnus (God Magnus) in ''Anime/TransformersRobotsInDisguise''/''Car Robots''. He's arrogant and bitter about Optimus being chosen to carry the Matrix instead of him, but he's no friend of the Predacons or Decepticons, and at least once rebuffs Scourge/Black Convoy outright when the latter thinks that just because he's Optimus' rival that it somehow makes him a bad guy. He just really, really wants the Matrix, and isn't above roughing up Optimus to get it, making him a third-party antagonist for much of his early appearances. In spite of his superiority complex, he's also not above saving humans, either, meaning that while Magnus comes off as a dick, he's still got a good spark somewhere beneath all that ego.
* Team Unicorn and Team Ragnarok of ''Anime/YuGiOh5Ds'' are {{Opposing Sports Team}}s competing against the protagonists, so the protagonists have to defeat them even though there's nothing evil or villainous about them -- they believe in ThePowerOfFriendship just like the heroes, they care about and protect each other, they fight fair, and they don't want to hurt anyone. If they weren't competing against the characters the story had been long been following already, they would be heroes.
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