* 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.]]
** 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]].
** This is utilized to a lesser extent with their anime counterparts. Sabrina is converted into something of a demonic witch who antagonizes Ash and co., while many others, such as Lt. Surge, Clair, and Skyla, are egotistical {{Jerkass}}es that have a bigoted or bullying demeanor regarding how they handle Pokémon. All of them [[DefeatEqualsFriendship make friends with the heroes]] in the end.
** In ''VideoGame/PokemonBlackAndWhite'', N is a very sympathetic AntiVillain with good intentions. 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.
** [[spoiler: In ''VideoGame/PokemonBlack2AndWhite2'', Colress, while still a scientist in the employ of Team Plasma, does encourage the player and even gives them a device needed to progress further in the game. In ''Pokémon Best Wishes 2 Episode N'', Colress is a far more malevolent character 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 accomplish his goals and please Ghetsis.]]
* Gendo Ikari from ''Anime/NeonGenesisEvangelion''. 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 kills a cat]]. This has been done to the point where fans have nicknamed him [[FanNickname Evil Manga Kaworu]].
** Inverted with the Israfel twins in ''[[NeonGenesisEvangelionCampusApocalypse Campus Apocalypse]]''. In the anime, Israfel is just as destructive as the other Angels. Here however, the male twin is the only Angel who cares enough to not harm innocent humans (even saving the lives of Toji and Hikari), while the female twin is an adorable little girl with a crush on Shinji and no idea she's even an Angel.
* In the ''MaiHime'' 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 ''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.
* In the 2003 ''Anime/FullMetalAlchemist'' anime, Basque Grand was transformed from the ReasonableAuthorityFigure and ColonelBadass that he was in the manga 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. However, all three of these cases were due to those characters not having been well established yet in the manga when the [[OvertookTheManga anime overtook it]].
** Particularly justified in the case of Basque Grand, since Hohenheim and Kimblee had the advantage of at least having brief appearances on screen in the manga before their introduction to the anime. Basque Grand was mentioned has having been killed off screen in the manga and nothing else, so the writers of the anime had nothing to go on with him besides his name, appearance, and occupation.
* 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).
** Reversed for Dr Eggman, who starts off an AffablyEvil villain near identical to his games counterpart, before softening more and more into something of a FriendlyEnemy of Sonic (this is taken UpToEleven in the comic adaptation).
* Kushana in the ''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.
* 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 was a sweet and simple YamatoNadeshiko in the original game... and then she became quite the infamous boxcutter-using {{Yandere}} in the anime.
* The Dark World Fiends were presented as villains in the second 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.
* 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.
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