Full story
The film opens at the White House. A blue-skinned teleporting mutant slips past the guards and nearly kills the President of the United States. It's Kurt Wagner, Nightcrawler, and someone was controlling him. The attack gives Colonel William Stryker, a military man obsessed with mutants, the green light to raid Xavier's school. Meanwhile, Logan comes back from Alkali Lake with no answers, and Jean Grey feels her power growing in ways she can't control.
Xavier and Cyclops visit Magneto in his plastic prison and learn that Stryker pulled information out of him with a serum. On the way back, both are captured. That same night, Stryker's troops storm the mansion and take several students. Logan protects the kids, and Iceman, Rogue and Pyro escape with him. Stryker claims to know Logan and hints that he helped make him. Mystique, in disguise, seduces a guard, injects metal into his blood and Magneto breaks out.
Storm and Jean find Nightcrawler, a gentle, religious former circus performer. Logan and the kids stop in Boston at Iceman's family home, where his parents never knew their son's secret. His brother calls the police, and Pyro loses it and turns his fire on the officers. The X-Men's jet is attacked, and Magneto shows up to save them. He offers a truce and lays out the plan: Stryker built a second Cerebro at Alkali Lake and will use his son Jason, a mind-controlling mutant, to force Xavier to kill every mutant on the planet.
Both groups break into the base. Wolverine finds the lab where he got his adamantium and fights Lady Deathstrike, who has claws and healing like his. He wins by injecting her with liquid adamantium. Jean beats a brainwashed Cyclops and ends up cracking the dam. Magneto and Mystique reach Cerebro but flip the target: now the machine will kill every human. Storm and Nightcrawler free Xavier and break Jason's hold. Magneto escapes with Mystique and takes Pyro with him. Stryker is left chained up and dies in the flood.
The dam bursts and the jet won't lift off. Jean steps outside, holds back the water with her mind and lifts the plane, staying behind. She vanishes into the lake. Xavier and the X-Men hand Stryker's files to the President and call for peace. In the final image, the shadow of a firebird appears under the surface of the lake.