The X-Men and Magneto are forced to stand together when the devious machinations of William Stryker threatens mutankind in the comic book adaptation of Bryan Singer's 2003 sequel to X-Men.
The teleporting mutant
Nightcrawler, having been brainwashed by the evil government operative
William Stryker, makes an attempt on the president's life.
Wolverine discovers nothing at the Alkali Lake facility, much to his disappointment.
Jean Grey and
Storm locate Nightcrawler with the help of
Professor X and
Cerebro, while the professor visits with
Magneto in the villain's plastic prison. Professor X learns from reading Magneto's mind that Stryker has been extracting information from the mutant, and Stryker springs a trap on the professor and
Cyclops with the help of assistant Yuriko Oyama, also known as
Lady Deathstrike.
The military raids the
Xavier Institute of Higher Learning, and begins to tranquilize every student they can. Wolverine intervenes, and Stryker makes some enigmatic allusions to their past together, but Wolverine and a handful of the students are forced to flee the school, or be captured.
Mystique infiltrates the prison disguised as Senator Robert Kelly and Lady Deathstrike, and aids Magneto in escaping from his prison cell. Wolverine heads to
Boston,
Massachusetts with
Rogue,
Pyro, and Bobby Drake, also known as
Iceman. Drake's brother calls the police, and the group is confronted as they are attempting to leave the Drake family home. After shooting Wolverine in the head, Pyro unleashes his pyrokinetic abilities on the officers. Rogue uses her own power to absorb Pyro's power, and douse the flames. Storm arrives with the
X-Jet, and the team regroups with their new allies, Magneto and Mystique. Magneto reveals to the X-Men that Stryker orchestrated the attack on the president, and has been secretly injecting mutants with a serum to control them. Jean reads Nightcrawler's mind, and determines that his base is located inside of a dam at Alkali Lake, where Stryker intends to build a second Cerebro to destroy every mutant on the planet.
Stryker is able to force Professor X to use Cerebro to find and kill the world's mutants by using his own son, a powerful telepath named Jason. Mystique infiltrates the compound by impersonating Wolverine, and the remaining members of the team follow her. Jean, Magneto, and Mystique are attacked by a brainwashed Cyclops, and in the process, damage the generators that prevent the dam from failing. Jean's telekinetic blast frees Cyclops from his brainwashing. Wolverine discovers Stryker and Lady Deathstrike in an
adamantium smelting room, and Wolverine battles Lady Deathstrike to the death. After defeating Deathstrike, Wolverine finds Stryker on a landing pad, chained to his helicopter by Magneto's power of magnetism. Stryker offers Wolverine clues to his past in exchange for his freedom, but the mutant returns to save his friends, leaving the government operative to his doom.
Mystique disguises herself as Stryker, and commands Jason to locate and kill all of the humans on earth. She and Magneto escape the compound in Stryker's helicopter, leaving the man chained to a pile of rubble. Nightcrawler teleports Storm into the secondary Cerebro chamber, allowing her to cause an ice storm that frees the professor from his mental possession. The damn bursts, but a mechanical failure aboard the X-Jet prevents the jet from taking off. Jean sacrifices herself by creating a telekinetic shield enabling the jet to take off, but is then consumed by the lake. Later, the X-Men visit the President in the oval office, and provide him with files from Stryker's office. He warns the man that humans and mutants must work together to create a peaceful co-existence based on tolerance, or risk an all-out war between the species. Back at Alkali Lake, the image of the
Phoenix appears over the calm waters.
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