For some odd reason, Wolverine and the X-Men is FULL of this (possibly because some of these characters would have returned as heroes had the second season been made).
- Domino is a member of the X-Force and the X-Men in the comics, but she is depicted as a terrorist and member of the Brotherhood of Mutants in the adaptation, which results in her basically being similar role to Mystique in all but her name, appearance, personality, and powers as Mystique herself is The Dragon to Magneto in some adaptations.
- Multiple Man is depicted in this adaptation as a member of Mr. Sinister's Marauders despite being a main character in X-Factor since the 90's.
- Likewise, the Stepford Cuckoos are shown in this series as villainous members of the Inner Circle Club despite being students at the Xavier Institute in the comics.
- Gambit at this point had been portrayed as a hero and loyal X-Men member in the comics for decades as well as a vitriolic Friendly Rival to Wolverine, in the show he's a Heel–Face Revolving Door Smug Snake who willingly works for Bolivar Trask. Logan even threatens to kill Gambit after he betrays him at the end of one episode. Particularly jarring for fans of the 90s show who were used to a traditionally heroic Gambit.
- Psylocke is a heroic member of the X-Men in the comics. In this adaptation, she assists the Brotherhood in one episode (although she's shown to be a reluctant recruit who only helps out the group because she owes Quicksilver a favor).
- Blink was associated with Generation X and was a member of the New Mutants. Her better-known alternate version rose from Age of Apocalypse mainstay to leader and main hero of the Exiles. In this adaptation, she is a member of Magneto's Acolytes, though she does send Magneto away under Scarlet Witch's orders in the season finale.
- Mercury was a member of the New X-Men in the comics. In this adaptation, she is a member of Magneto's Acolytes.
- In the comics, Scarlet Witch and Quicksilver were former members of the Brotherhood of Mutants who abandoned Magneto very quickly and joined The Avengers. In this adaptation, Quicksilver is still a member of the Brotherhood while Scarlet Witch is loyal to her dad (although it isn't until the finale that she finally realizes what a monster Magneto is and turns against him).
- Zig-zagged with Magneto himself. While he wasn't a villain in the comics at the time the show was released, there are over 3 decades (60's, 70's and 90's) of comics where he was the villain meaning the show wasn't exactly pulling its villainous portrayal of him out of its ass. Also Magneto's treatment of his children in the show is conversely far better than the comic version (at least towards Scarlet Witch and Polaris), who's easily one of the worst dads in Marvel.
- Emma Frost. Just like Magneto, she used to be one hell of a foe (even being Big Bad of New Mutants for a time) but comic fans know that that was a long time ago, at least in the main Marvel Universe. In this show, she's The Mole and still the White Queen of the Hellfire Club. However, she sacrifices her life to contain the Phoenix in the series finale.
- The Phoenix. This is far from the first adaptation to do so, but it's worth mentioning that in the comics, Jean as Phoenix was good but Anti-Hero-ish, had to resist darker impulses but stayed in control (she was actually Phoenix for quite some time), and even saved the universe. It took the Hellfire/Inner Circle Club's interference to cause her to become Dark Phoenix. This adaptation uses The Theme Park Version where the Phoenix is a 100% Bad Thing. Of course, the Inner Circle Club was trying to control the Phoenix in this version, intending to extract it from Jean so the Stepford Cuckoos could then use its power, but it wasn't quite the same as Jason Wyngarde and Emma Frost putting her under More than Mind Control and pretty much breaking down her self-control bit by bit until we got a monster.
