In the not so distant future, various people with genetic mutations are considered freaks and/or dangerous aberrations. One McCarthyesque politician, U.S. Senator Robert Kelly (BRUCE DAVISON), even wants to impose legislation designed to expose all such people.
Among them is Professor Charles Xavier (PATRICK STEWART) the telepathic, wheelchair-bound leader of the X-Men, a group of mutants whose purpose is to protect and teach their own kind about how to survive in a world where they're the definite minority. Among Xavier's longtime students is Cyclops (JAMES MARSDEN), a man whose eyes emit laser blasts; Jean Grey (FAMKE JANSSEN) another telepathic mutant with telekinetic powers; and Storm (HALLE BERRY) who can manipulate and control the weather.
Xavier's counterpart is Magneto (IAN McKELLEN), a man who, despite his powerful control over magnetism, couldn't escape the horrors and prejudice of WWII era concentration camps. As such, and feeling prosecuted once again, he's determined to avoid and/or control such hate from surfacing once more. Among his devoted followers are Sabretooth (TYLER MANE), a gargantuan and seemingly undefeatable giant of a man; Toad (RAY PARK) whose physical abilities mimic his namesake species; and Mystique (REBECCA ROMIJN-STAMOS) a blue-skinned mutant who can transform herself into anyone else.
When loner mutants Wolverine (HUGH JACKMAN), a man with retractable claws and the ability to heal quickly, and Rogue (ANNA PAQUIN) an alienated teenage girl who can absorb the powers of and thus kill anyone she touches, are attacked by Magneto's cronies, Xavier begins to question what his former acquaintance might be planning.
Upon learning that Magneto's diabolical plan involves Rogue and an upcoming United Nations Summit meeting, Xavier and his team set out to stop the mutant terrorists before they harm others and cause even further problems with their human counterparts.