- Directors: Bryan Singer
- Producers: Tom DeSanto, Avi Arad, Bryan Singer, Ralph Winter, Lauren Shuler Donner
- Writers: Screenplay, Michael Dougherty, Dan Harris, David Hayter, Story, David Hayter, Bryan Singer, Zak Penn, Comic Book, Stan Lee, Jack Kirby
- Genres: Action, Adventure, Sci-Fi, Thriller
- Actors: Hugh Jackman, Patrick Stewart, Ian McKellen, Famke Janssen, Brian Cox, Alan Cumming, Anna Paquin, Halle Berry, Shawn Ashmore, James Marsden
Nightcrawler, a teleporting mutant, attempts to assassinate the President in the White House, but he fails and escapes. Wolverine reappears after discovering nothing at Alkali Lake, while Storm and Jean find Nightcrawler with the help of Professor Xavier and Cerebro. 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 by Stryker and his assistant Yuriko Oyama. A military raid of the X-Mansion begins, with the soldiers sedating every student they find; some escape, while Wolverine finds Stryker, but is unable to find anything about his past.
Impersonating Senator Robert Kelly and Yuriko, Mystique gains information about Magneto’s prison and provides a means for him to escape. Wolverine, along with Rogue, Iceman and Pyro, heads to Iceman’s home in Boston. After a 9-1-1 call by Bobby’s brother Ronnie, the police arrive just as the group is about to leave, ensuing into a dispute with Pyro. The X-Jet arrives to pick them all up, and the X-Men team with Magneto and Mystique. Magneto has learned Stryker orchestrated the attack on the President and has been experimenting on mutants, using a drug injected directly into the back of the neck to control them. Jean reads Nightcrawler’s mind and determines that Stryker’s base is located at Alkali Lake, inside the dam. He has also stolen enough equipment from Xavier’s own Cerebro unit to build a second Cerebro, with which he plans to kill all the world’s mutants.
Mystique, disguised as Stryker, uses Jason to convince Professor X to kill all humans. Magneto and Mystique use Stryker’s helicopter to escape Alkali Lake, chaining Stryker to concrete rubble, and are also joined by Pyro. Meanwhile, Nightcrawler teleports Storm inside of Cerebro, 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. The X-Men are able to supply the President with files from Stryker’s private offices, and Professor X warns him that humans and mutants must work together to build peace, or they will destroy each other through war. The film ends with a voiceover by Jean Grey on the process of evolution (a speech originally made by Professor Xavier in the introduction of the first film). The camera floats over Alkali Lake, showing a vague shape of a Phoenix in the lake.