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.