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.

After the re-emergence of the world's first mutant, world-destroyer Apocalypse, the X-Men must unite to defeat his extinction level plan.

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

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 organised under Xavier's former ally, Magneto.