The mutants : Their existence is known. They have aroused fear, distrust and hatred. The debate divides the planet. Are the mutant representing the next step of evolution or does it concerns a new parallel humanity that claims its part of this world. Anyway, it an historical fact: sharing the world has never been the vocation of mankind.
Mutants continue their struggle against the society that fears and distrusts them. Their cause becomes even more desperate following an incredible attack by an as yet undetermined assailant possessing extraordinary abilities. The shocking attack renews the political and public outcry for a Mutant Registration Act and an anti-mutant movement now led by William Stryker, a wealthy former Army commander who is rumored to have experimented on mutants.
Stryker's mutant « work » is somehow tied to Logan's mysterious and forgotten past. As Wolverine searches for clues to his origin, Stryker puts into motion his anti-mutant program. While Tornado and Jean Grey are searching for the author of the attack against the President, he launches an attack on Xavier's mansion. Alone to defend the center, Logan succeeds in escaping with most of children. Nethertheless, Stryker captures a prey of choice, Professor Xavier. He uses on him the exceptional power of his son Jason, formerly one of Xavier's pupil, to oblige him the use of the « Cerebro ». This machine, Xavier is the only able to fit, allows him to notice and to contact each being on the planet. Stryker plans to use the professor's power to destroy all the mutant.
Magneto, newly escaped from his plastic prison, proposes a partnership with the X-Men to combat their common and formidable enemy. Together, they fly to Xavier rescue and to stop Stryker who has built a second Cerebro in his secret base situated under an hydraulic barrage.
Thanks to her polymorphous abilities, Mystique gets infiltrate in the base with the other mutants. Logan throws to Stryker's pursuit. It is important for him to get the answer to the questions he was always wondering. Where is he coming from? Who is he? Stryker is although the one who created Volverine, but he is not unique. Deathstrike, his assistant is equally a faithfull Stryker's creation.
Through Jason, Stryker has begun to manipulate Xavier and to exterminate the mutants. Helped by their new friend Nightcrawler, a mutant with teleport abilities, implied in the attack against the President, Tornado enters the Cerebro. She uses all the energy of her power to stop Jason. But if the mutant are saved, humans are now threatened when Magneto reverses the movement and uses now Xavier to destroy the human…
Spoiler ! the end of the story is revealed below…
Fortunately, Xavier is pulled out of the Cerebro just in time before the explosion of the barrage. Jean Grey sacrifices herself to save the rest of the team Magneto left besides. Humanity is once more saved, so are the mutants. Xavier goes on a rendez-vous with the President of the United States to reveal him the truth on Stryker and his terrible plot, exulting him to help humans and mutants to live together…
The X-MEN are back, more powerfull but also more numerous. A new generation allies to the X-Men to confront the terrible threat that represents Stryker et Deathstrike. The crew now officialy includes Alicia, who absorbe the energy of those she touches, Iceberg who masters cold and ice and Pyro who, in the other side has this ability to handle fire without producing it. In this new chapter, the threat doesn't come from a powerfull mutant but from a human.