A mutant named Nightcrawler attempts to assassinate President McKenna, but he fails when he seems to come to his senses. Jean is confronted by Cyclops, where she admits she has been having bad feelings about the future. Wolverine reappears after discovering nothing at Alkali Lake and is immediately asked to look after the children of the school. After some difficulty, Professor Xavier locates Nightcrawler with Cerebro and sends Storm and Jean to retrieve him. They find Nightcrawler who willingly leaves with them, explaining that he had no control over his actions in the White House. Cyclops and Professor X visit Magneto in his plastic prison to see if he had any part in the attack on the President. Reading Magneto's mind, Professor X discovers that a covert government operative, William Stryker, has been extracting information from Magneto. A trap is sprung and Cyclops and Professor X are captured via Stryker and Lady Deathstrike. A military invasion of the school begins, with the soldiers sedating every mutant they find. Siryn wakes everybody up with one of her sonic screams and Colossus and Wolverine round up a number of the students. Wolverine stays behind to confront the attackers, and finds them led by William Stryker. Stryker offers Wolverine the truth about his past, but before Wolverine answers, Iceman creates a thick wall of ice between them.
Impersonating Senator Robert Kelly, and Stryker's assistant Yuriko Oyama, Mystique gains information about Magneto's prison and provides a means for him to escape. Mystique tricks one of Magneto's Security Guards, implanting large amounts of iron in his body which was later on extracted by Magneto via force of magnetism. Wolverine, along with Pyro, Iceman and Rogue, heads to Iceman's home in Boston. The police arrive just as the group is about to leave. After a policeman shoots Wolverine in the head, Pyro begins using his abilities to attack the officers and destroy their cars. Rogue manages to stop him just as the X-Jet arrives to pick them all up. The X-Jet is targeted by two Air Force fighter jets who attempt to force a landing. After the X-Jet refuses to land, the pilots fire missiles. Storm tries to distract the pilots with several tornadoes but the last pilot fires two missiles. Jean is able to destroy one of the missiles, but the other detonates directly behind the jet. The jet, en route to a crash landing, is stopped at the last moment by Magneto, who is standing on the ground. Magneto has learned that Stryker orchestrated the attack on the President, and has been experimenting on mutants. Jean Grey reads Nightcrawler's mind and determines that Stryker's base is located at Alkali Lake, inside the dam. Stryker has been using a drug, injected directly into the back of the neck, to control mutants. He has also stolen enough equipment from Xavier's own Cerebro unit to build a second Cerebro; he plans to use Professor X to kill all of the mutants in the world. The X-Men and Magneto join together in an effort to stop Stryker. On the way to Alkali Lake, Pyro has a conversation with Magneto about how the world perceives them.
Stryker gains control over Professor Xavier through his son, Jason Stryker, who is able to project powerful visions in the mind, blinding a person to reality. Professor X is instructed to use Cerebro to find and kill all existing mutants. Mystique infiltrates the base disguised as Wolverine. Mystique manages to take over the control room, opening up the main gates for the X-Men. Storm and Nightcrawler pair off, searching for the kidnapped students. Jean, Magneto, and Mystique are attacked by a brainwashed Cyclops on their way to rescue Professor X. Cyclops' optic blast causes damage to the generators that keep the dam from collapsing. Jean gets Cyclops to return to his normal self by telling him she loves him. Wolverine finds Stryker in an adamantium smelting room along with Lady Deathstrike. Wolverine and Lady Deathstrike begin fighting, which ends with Wolverine pumping Deathstrike full of molten adamantium metal, killing her. Wolverine finds Stryker on a landing pad and stabs him in the stomach. Stryker attempts to bargain with Wolverine, telling him that if he comes with him he can tell him about his past. Wolverine refuses and straps the wounded Stryker to the helicopter wheel. Mystique, disguised as Stryker, uses Jason to convince Professor X to kill all humans. Magneto and Mystique escape on the helicopter, alongside with Pyro who has decided to join them. Meanwhile, Nightcrawler teleports Storm inside of Cerebro, from where she frees the Professor from his telepathic illusion. A malfunction aboard the X-Jet prevents it from taking off and the dam finally bursts. The flood gets stronger, drowning Stryker. Jean leaves the jet and creates a telekinetic wall in order to stop the wave, and at the same time raises the jet above the flood waters; all the while surrounded by a corona of fire. Jean activates the X-Jet's primary engines, before releasing the torrent of water down on herself.
Back at the White House, the President prepares to address the country on the perceived mutant threat. Just as he begins his speech the X-Men appear before him. Rogue gives him the files from Stryker's private offices while Professor X tells him about the events of the last few days. Then Professor X warns him that humans and mutants must work together to build peace, or they will destroy each other through war. Back at the mansion, Xavier states that Jean Grey always felt left behind compared to others. Wolverine then reveals to Cyclops that Jean Grey truly loved Scott, and chose to be with him. The film ends with a voiceover by Jean Grey, on the process of evolution. The camera floats over Alkali Lake, showing a vague shape of a Phoenix in the lake.
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