Wolverine comes to Japan to meet an old friend whose life he saved years ago, and gets embroiled in a conspiracy involving yakuza and mutants.

In a world where mutants (evolved super-powered humans) exist and are discriminated against, two groups form for an inevitable clash: the supremacist Brotherhood, and the pacifist X-Men.

When anti-mutant Colonel William Stryker kidnaps Professor X and attacks his school, the X-Men must ally with their archenemy Magneto to stop him.