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.

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.

Wolverine faces his ultimate nemesis - and tests of his physical, emotional, and mortal limits - in a life-changing voyage to modern-day Japan.

万磁王为了争取更多变种人的权利，他聚集了一批部下不断针对人类进行破坏。而X教授致力于人类与变种人之间和谐生存，他创办了X学院，收取变种人学生，教导他们知识，让他们能合理运用自己的能力。培养他们成为X战警，保卫人类与变种人。

Professor Charles Francis Xavier, who has the mutant ability to read minds, searches for new mutants to train them how to use their powers for good and to prevent the mutants from harming themselves and others at his School for Gifted Youngsters. His opposition, Magneto "Master of Magnetism", is doing the same thing, but for evil purposes. He has made Mystique who is a shape-shifter, a principle of his high school to gather evil mutants to prepare them for war against non-mutants. The most interesting plot of the story is that all the heroes and villains attend the same high school. The classic battle of good vs. evil has begun again.

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