Set 5 years after the end of Superman II, the film begins when Superman returns to discover his absence allowed Lex Luthor to walk free, and that those he was closest too felt abandoned and have moved on. Luthor plots his ultimate revenge that could see millions killed and change the face of the planet forever, as well as ridding himself of the caped crusader.

When a cure is found to treat mutations, lines are drawn amongst the X-Men, led by Professor Charles Xavier, and the Brotherhood, a band of powerful mutants organized under Xavier's former ally, Magneto.

Professor Charles Xavier and his team of genetically gifted superheroes face a rising tide of anti-mutant sentiment led by Col. William Stryker in this sequel to the Marvel Comics-based blockbuster X-Men. Storm, Wolverine and Jean Grey must join their usual nemeses Magneto and Mystique to unhinge Stryker's scheme to exterminate all mutants.

Two mutants, Rogue and Wolverine, come to a private academy for their kind whose resident superhero team, the X-Men, must oppose a terrorist organization with similar powers.