* In the ''Anime/VisionOfEscaflowne'' movie, Folken is a psychotic BigBad, while in the original series he was more of an AntiVillain or a DragonWithAnAgenda to the actual BigBad, Emperor Dornkirk (who is absent from the movie altogether). [[spoiler: In fact, in the series he eventually has a HeelFaceTurn.]]
* To a lesser extent, King Dedede of ''Anime/KirbyOfTheStars''. While still rarely exceeding a petty comedic {{Jerkass}}, his anime counterpart has far fewer [[PetTheDog benevolent moments]] than that of the [[{{Kirby}} original games]] (who leans more as an AntiVillain - he is known to [[EnemyMine occasionally team up with Kirby against a more serious threat, such as Zero or Nightmare]], and is more greedy and selfish than outright evil) and usually plays the main antagonist of each episode.
* Some of the Gym Leaders and Elite Four members in ''Anime/{{Pokemon}}''. While most of them (with the exception of Giovanni) are good guys in the games - Lance and Lorelei even helping out the player character at key points - Lt. Surge, Koga, Sabrina, Agatha, Bruno, Lorelei, Lance, Karen, Will and [[spoiler: Pryce]] became villains in the manga adaptation ''Manga/PokemonSpecial''. [[spoiler:To be fair, though, Pryce is a more sympathetic AntiVillain, Lance is a WellIntentionedExtremist, and most of the other characters listed [[HeelFaceTurn reform]] later on, with the exception of Agatha.]]
** This is utilized to a lesser extent with their [[Anime/{{Pokemon}} anime]] counterparts. Sabrina is converted into something of a demonic witch who antagonizes Ash and co., while many others, most notably Lt. Surge, Erika, and Skyla, are egotistical {{Jerkass}}es with a condescending demeanor towards their challengers (or, in Erika's case, towards those who don't appreciate the perfume her gym makes). All of them [[DefeatEqualsFriendship make friends with the heroes]] in the end. However, others, like Brock, Misty, Cilan, Iris, and Clemont, join Ash as protagonists and are more openly heroic characters.
** ''Manga/PokemonSpecial'' has a downplayed example with Norman. In the games, Norman is a kind, gentle person who respects his child's wishes and would most likely not use physical violence. In the manga, Norman is a lot meaner and beats up his son for disobeying him. Despite his harshness, he is on the side of good - he is genuinely supportive of Ruby.
** And occasionally the Pokémon themselves (particularly either [[PoisonIsEvil Poison]] or [[DarkIsEvil Dark]] types), such as in the ''[[VideoGame/PokemonMysteryDungeon Mystery Dungeon]]'' games. In the games and anime, even Pokémon seen working for the antagonists aren't actually evil, [[PunchClockVillain just taking orders from their trainers]]. However, even in Mystery Dungeon, you can recruit Pokemon like Ekans and Skuntank into your team and the species itself isn't AlwaysChaoticEvil.
** At the end of {{VideoGame/PokemonRubyAndSapphire}}, Archie and/or Maxie are ObliviouslyEvil [[WellIntentionedExtremist Well-Intentioned Extremists]] and have a HeelRealization once they see the true effects of their plans and quickly HeelFaceTurn. In ''Special'', neither one reforms - they go into SanitySlippage and [[spoiler: are both KilledOffForReal]]. Maxie even [[spoiler: outright ''kills'' Norman (although Norman [[CosmicRetcon gets better]])]].
** In ''VideoGame/PokemonBlackAndWhite'', N is a very sympathetic AntiVillain with good intentions. He eventually makes a HeelFaceTurn in the sequel games, helping the player against Ghetsis, his much more evil adoptive father. However, in ''Manga/PokemonSpecial'', N has fewer redeeming qualities and manages to convince White's Tepig to leave her. His goal also seems to be more like Ghetsis' goal than in the games.
** In ''VideoGame/PokemonBlack2AndWhite2'', Colress, while still a scientist in the employ of Team Plasma, does [[FriendlyEnemy encourage]] the player and even gives them a device needed to progress further in the game. He is involved with Team Plasma ForScience and is not particularly interested in their goals, expressing distaste for Ghetsis. After his defeat, he encourages the player to stop Ghetsis' plans. In ''[[Anime/{{Pokemon}} Pokémon Best Wishes 2 Episode N]]'', Colress is a true MadScientist who experiments on Pokémon to the point of torture, uses mind control on the Pokémon in his introductory episode (including those of the main characters), and is more than willing to hurt Ash and his friends to prove his theories. He is also more appreciative of Ghetsis due to Plasma's "providing" increasingly more difficult "subjects" pushing the theories further. Colress in the game has a HeelFaceTurn, willingly disbands Team Plasma, and becomes TheAtoner after Ghetsis is defeated, while his anime counterpart is arrested by Looker. The Anime counterpart does come up with the idea for a [[SpeaksFluentAnimal Pokemon translator]], but after he's arrested and in a way emphasising his BlueAndOrangeMorality.
** The ''Manga/PokemonSpecial'' version of Colress is portrayed along the same lines as in the anime.
* ''Anime/NeonGenesisEvangelion'':
** Gendo Ikari: In the anime, he is AmbiguouslyEvil, he sincerely praises Shinji for his combat performance at one occasion, and with his FamousLastWords he regrets having been a bad father to him. In the manga adaptation, he is unquestionably evil, has a [[GodIsEvil massive]] [[AGodAmI God-complex]], and outright hates Shinji. In the manga, he's also implied to have [[spoiler: personally killed Kaji]], whereas it was unknown if he had anything to do with it in the anime, even though he was hinted at being involved somehow. He's somehow even ''worse'' in ''[[NeonGenesisEvangelionCampusApocalypse Campus Apocalypse]]''.
** To a smaller extent, Kaworu. In the original anime, he was pretty nice (outside of, you know, [[spoiler:being the seventeenth Angel]]). In the manga, he [[KickTheDog strangles an abandoned kitten]] (a scene infamous enough to earn him the nickname [[FanNickname "Evil Manga Kaworu"]]) and has a much stronger case of BlueAndOrangeMorality.
* In the ''Manga/{{Mai-HiME}}'' manga, the main antagonists of the first arc are Haruka and Yukino, the latter of whom is friends with Mai and Mikoto in the anime, and the otherwise heroic Akira assists them. By contrast, Shizuru never turns PsychoLesbian, and Nao ([[TeethClenchedTeamwork reluctantly]]) helps the heroes after the teams merge.
* In the ''Manga/MaiOtome'' manga, Tomoe is DemotedToExtra and does not attempt to plot against Arika, and Nina never does a FaceHeelTurn. On the opposite end, Sergey goes from a PunchClockVillain who betrays the BigBad for his daughter's sake to a BigBad who is not related to Nina, biologically or otherwise.
* The 2003 ''Anime/FullMetalAlchemist'' anime has several cases that were due to those characters not having been well established yet in the manga when the [[OvertookTheManga anime overtook it]]. Basque Grand was transformed from a ReasonableAuthorityFigure and ColonelBadass into a ColonelKilgore and GeneralRipper who just can't wait to commit some more genocide. Kimblee, while an awful person in the manga, had his negative qualities cranked UpToEleven, and his good ones suppressed. Even Hohenheim, the BigGood in the manga, became a RetiredMonster; instead of being [[UnwittingPawn tricked]] into helping Father turn the nation of Xerxes into a Philosopher's stone, and only becoming aware of the plan once it was too late to stop it, he and Dante turned people into Philosopher's Stones to prolong their lives.
** Wrath and Envy were already horrible monsters in the manga, but the anime made them worse. Wrath (now named Pride) loses all of his NobleDemon qualities and his last scene involves him ''strangling his MoralityPet'', Envy had his sadism cranked to maximum, and both lose their AlasPoorVillain moments.
* In a similar but lesser manner, Shadow the Hedgehog in the ''SonicX'' anime. In the games, Shadow started off a vengeful weapon ready to destroy Earth's population in honor of his murdered friend. Throughout his story however, he is portrayed with a palpable sense of doubt and emotional conflict, before ultimately pulling a full HeelFaceTurn two games later. In the anime, he roughly follows his games counterpart's story, but maintains his more sinister neutral alliance and is TheUnfettered to the highest scale (at least once perfectly willing to kill a child in cold blood, along with anyone who defended her, if it meant stopping a BiggerBad).
* Kushana in the ''Manga/NausicaaOfTheValleyOfTheWind'' manga is introduced as an antagonist, but it's more a case of her goals not aligning with the protagonists, and when circumstances change she ends up [[HeelFaceTurn an ally to Nausicaä]]. In TheMovie, she's the main villain.
* Ho Yinsen in the ''Anime/IronMan'' anime. Though near the end it turns out he's technically BrainwashedAndCrazy.
** Black Widow and Hawkeye are usually depicted in both the 616 and Ultimate universes as AntiHero allies of SHIELD. TheMovie ''Rise Of The Technovore'' depicts them as much more antagonistic and villainous.
* In the manga of ''Manga/DeadmanWonderland'', the staff of the titular prison HandWave the prisoner deaths in the dog races by claiming that they are done with special effects. In the anime, the special effects angle is done away with; and the prison openly admits that many of the competitors do not survive and die brutal deaths.
* Kaede Fuyou from {{Shuffle}}. While ''not'' exactly a villainess, she did, in both versions, believe that Rin was responsible for her mother's death (a misconception he encouraged to prevent her from losing the will to live), and abused him for years until learning the truth, at which point she devoted herself to him in order to atone. In the anime, in which Rin canonically goes out with their mutual friend and [[SenpaiKohai senpai]], Asa, resulting in him spending less time with Kaede (in part not wanting her to be consumed with him), she snaps and attacks Asa, causing her to collapse, but comes to regret this later. In the visual novel, after finding out that Rin and Asa are a couple, Asa apologizes, but Kaede sadly accepts their relationship, albeit with the scene being somewhat similar to Kaede and Asa's reconciliation from the anime.
* The Dark World Fiends were presented as villains in the third season of ''Anime/YuGiOhGX'', which contradicts the flavor text of some of their cards in the game and the ''Master Guide 2'', which claims they are not evil. In fact, the flavor text on [[http://yugioh.wikia.com/wiki/Zure,_Knight_of_Dark_World Zure, Knight of Dark World's]] card claims that he "never oppresses the commoners", while that's probably what he's most notorious for doing in the anime.
** Also, in the manga version, Jim Cook is an antagonist who is far more malicious than his lighthearted and benign anime counterpart. [[spoiler:It's not his fault, however; he's a BrainwashedAndCrazy pawn of [[BigBad Tragoedia]].]]
* In the manga version of ''Anime/YuGiOh5Ds'', pretty much every character has a different background and personality, but Rua and Ruka more so than any other. They start of as villains in this version (and rather sadistic ones at that) ''very'' unlike the kind and innocent children they are in the anime. It is later revealed that [[spoiler:Rua underwent a [[DealWithTheDevil Duel Dragon ceremony]] to save Ruka from an illness, only Luna to become enslaved by the spirit of one of the Duel Dragons and for Rua to become {{Brainwashed}} by ''her''. Eventually, Yusei is able to use his more benevolent Dragon to break the spell.]]
* In the manga version of ''ChronoCrusade'', BigBad Aion is portrayed as misguided and possibly insane, but sympathetic, having turned to evil deeds in a desperate attempt to fix what he felt was a corrupted system after learning an AwfulTruth. In the anime, he was turned into the literal AntiChrist.
* ''{{Pretear}}'': In the manga version, one of the Leafe Knights ([[spoiler: Sasame, the Knight of Sound]]) is strongly hinted to have been in love with the villain in the backstory, but he's definitively a good guy and remains that way for the entire story. In the anime, where Fenrir plays a bigger role, he eventually breaks down and becomes her minion because of his MadLove.
* [[MadScientist Dr. Stein]] in ''Manga/SoulEater''. In the manga, he's [[SociopathicHero semi-sociopathic]], [[TheCorruptible prone to insanity]], and [[AxCrazy rather disturbing even when he's sane-ish.]] However, he's still good throughout, [[spoiler: even when Medusa begins artificially enhancing his madness]], and clearly cares about his students and teammates. In the anime, however, [[spoiler: he temporarily goes over to Medusa's side and even attacks [[MoralityChain Marie.]]]]
* ''Anime/BombermanJetters'' famously changed Max from a FriendlyRival into a ruthless villain.
* Queen Beryl of ''Franchise/SailorMoon'' was a villain in [[Manga/SailorMoon the manga]], but an ultimately tragic figure who was manipulated by Metaria into her crimes in her past and current incarnations, and ultimately doomed not by her villainy, but her own belief that she was beyond redemption at this point. In TheNineties [[Anime/SailorMoon anime]], she's a straight-up evil villain who willingly and loyally serves Metalia.
* The first anime of ''BlackButler'' does this with Queen Victoria, of all people. In the manga she's a straight CoolOldLady [[spoiler: though she seems to like the idea of a Zombie army]], while in the anime she's [[spoiler:responsible for Ciel's parents' deaths, and planning to start a world war to "cleanse" the world with her angelic accomplice, Ash]].
* Char Aznable from the original ''MobileSuitGundam'' and its sequels certainly had his faults (up to and including [[CharsCounterattack that time he tried to blow up the Earth]]), but ''MobileSuitGundamTheOrigin'' manages to up the ante even further by making him a freakin' ''[[RapeIsASpecialKindOfEvil rapist]]''.
* ''Anime/VariableGeo'' does this with [[LipstickLesbian Ayako's]] character. In [[VideoGame/AdvancedVariableGeo the game series]] which the OVA is based on, she protects women by luring out would-be muggers and rapist and brining them to justice. By contrast, the anime [[DepravedHomosexual practically makes Ayako a rapist, herself]], by having her sexually harass Satomi during their fight. She not only shreds Satomi's uniform, using [[CombatHandFan a hidden blade]], she even gropes Satomi and pecks her on the cheek. For Satomi, ''[[RageBreakingPoint that]]'' [[KillItWithFire was the last straw.]]
* The [[Literature/AliceInWonderland Cheshire Cat]] in the manga adaptation of the ''Manga/KingdomHearts'' series is outright villainous, compared to his more neutral role in his origin book and in the game. Maleficent even offered him a place in her group, but he declined.
** He's at his worst in the manga adaptation for ''Manga/KingdomHearts358DaysOver2'': Roxas wished to be let out of a cage he was imprisoned in for trespassing the White Rabbit's house and pretending to be his servant, Mary Ann. The Cheshire Cat granted his wish by [[JackassGenie throwing a hedgehog at the Queen of Hearts]] and [[MoralEventHorizon framing Roxas for the crime]], causing her to order the young Nobody's execution by [[OffWithHisHead guillotine]].
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