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X2: X-Men United (X2)
At the White House, a teleporting mutant, Nightcrawler, attacks the President of the United States; he is shot and retreats. Meanwhile, Logan explores an abandoned military installation at Alkali Lake in Alberta for clues to his past, but finds nothing. Jean Grey has been having premonitions and struggles to concentrate as her powers become increasingly difficult to control.
Later, Logan returns to Professor Xavier 's school for mutants, and Xavier tracks Nightcrawler using Cerebro. Xavier and Cyclops go to question the imprisoned Magneto about the attack, while Jean and Storm retrieve Nightcrawler. Military scientist Colonel William Stryker approaches the President and receives approval to investigate Xavier's mansion for their ties to mutants after the recent attack. Stryker's forces invade the school and abduct some of the students. Colossus leads the remaining students to safety while Logan, Rogue, Iceman, and Pyro escape. Stryker's assistant Yuriko Oyama captures Cyclops and Xavier. During the attack, Logan confronts Stryker, who addresses him as "Wolverine" and appears to be aware of his past.
The shapeshifting mutant, Mystique, helps Magneto escape and finds Cerebro schematics. Logan, Rogue, Iceman, and Pyro visit Iceman's family in Boston. Iceman's brother calls the police after learning he's a mutant. Officers surround the house; one shoots Logan after feeling threatened. Pyro fights back against officers with his pyrokinesis before Storm, Jean, and Nightcrawler pick them up in their jet.
The X-Jet is attacked by fighter jets and shot down while returning to the mansion, but Magneto saves them. He explains that Stryker built a second Cerebro to kill every mutant telepathically, using his mutant son Jason, who can control minds, to coerce Xavier. Stryker previously used Jason's powers on Nightcrawler to attack the White House to justify his excuse for invading Xavier's mansion. Magneto also tells Logan that Stryker grafted adamantium onto his bones and caused his amnesia. Jean discovers Stryker's underground base in a dam at Alkali Lake.
Disguised as Logan, Mystique infiltrates Stryker's base, letting mutants in while she and Magneto head to disable Cerebro before Xavier, brainwashed, can activate it. Storm and Nightcrawler rescue students, and Jean fights a mind-controlled Cyclops; their fight frees Cyclops but damages the dam, causing it to rupture. Logan finds Stryker in an adamantium smelting lab, recalling where he got his skeleton. Logan fights and kills Yuriko, then chases Stryker to a helicopter pad and chains him to the wheel. Magneto stops Cerebro and, with Mystique impersonating Stryker to command Jason, has Xavier redirect its powers on humans. They escape in Stryker's helicopter, and Pyro, swayed to Magneto, joins them. Nightcrawler teleports Storm inside Cerebro, where she creates a snowstorm to break Jason's concentration and free Xavier.
The X-Men flee the dam as water engulfs it, killing Stryker, but their X-Jet loses power and struggles to take off as floodwaters approach. Jean sneaks off, telepathically says goodbye, and holds back the water—raising the jet above it with flames erupting from her body—until she releases and the flood crashes down on her. The X-Men give Stryker's files to the President, with Xavier warning that humans and mutants must unite for peace. At the school, Xavier, Cyclops, and Logan remember Jean as Xavier begins a class. Meanwhile, a Phoenix-like shape rises from flooded Alkali Lake.