X-Men is a side-scrolling action game based on the comic book series of the same name. The player can control one of four playable characters: Gambit, Nightcrawler, Wolverine, or Cyclops. In addition, it is possible to call upon four other X-Men in when necessary.

Professor X's Danger Room is a training facility that can fully re-create environments in which the X-Men can practice their powers, similarly to the holodeck in Star Trek. One day, the danger room starts to go crazy, and randomly loading up dangerous simulations. It turns out that Magneto, the leader of the mutant Brotherhood and the main adversary of the X-men, has loaded a virus into the Danger Room's computer, and now the X-Men have to stop it.