With his former friend and then nemesis, Magneto (IAN McKELLEN), imprisoned in a facility with no metal he can control, Professor Charles Xavier (PATRICK STEWART) hopes that things can return to normal, at least as much as possible for his school of mutants who are a minority in a world filled with prejudice against him.
His longtime associates - telepath Jean Grey (FAMKE JANSSEN), the weather controlling Storm (HALLE BERRY) and laser beam emitting Cyclops (JAMES MARSDEN) - are now guiding a new set of students. Among them are Pyro (AARON STANFORD), a teen who can control but not create fire and Bobby a.k.a. Iceman (SHAWN ASHMORE), who can instantly freeze anything. That doesn't include the heart of fellow mutant Rogue (ANNA PAQUIN) who's smitten with him, but wary of making contact since that might kill him.
The stability is short-lived, however, when another mutant, Kurt Wagner a.k.a. Nightcrawler (ALAN CUMMING), makes an apparent attempt on the President's life. That results in a high-level meeting with Senator Kelly (BRUCE DAVISON) and military man William Stryker (BRIAN COX).
Despite having a mutant, Yuriko Oyama, a.k.a. Deathstrike (KELLY HU), as his assistant, Stryker has a grudge against their kind due to Xavier's former dealings with his son Jason (MICHAEL REID MACKAY). He also has a background with Wolverine (HUGH JACKMAN), a brooding mutant that Xavier has sent off on a reconnaissance mission.
While Storm and Jean Grey are off retrieving Nightcrawler, Wolverine returns to the school only to find Stryker's forces raiding it and kidnapping some of the younger students. Stryker also kidnaps Xavier, using his son to probe the professor's mind in hopes of operating a powerful device, Cerebro, which could be used to locate and kill all mutants on Earth.
With Magneto's shape-shifting assistant, Mystique (REBECCA ROMIJN-STAMOS), freeing him from his confines, the rest of the X-Men make an unlikely alliance with their former enemies, all in hopes of finding and stopping Stryker before he can enact his deadly and devastating plan.