Senator Robert Jefferson Kelly (Bruce Davison), a demagogue who would have made Hitler proud, has a solution to the "problem" of mutants. He wants a law that would require they all register with the government. Opposing him are two of the very people he condemns: Professor Charles Xavier (Patrick Stewart), who operates a school for "gifted children" where he trains young mutants to control their powers, and Eric Magnus Lehnsherr (Ian McKellen), a concentration camp survivor who foresees an oncoming war between human and mutant and intends to be on the winning side.
In the far northern reaches of Canada, a young runaway mutant who calls herself "Rogue" (Anna Paquin) encounters fellow mutant Logan (Hugh Jackman), an outcast known as Wolverine who earns his way with bare-knuckle fighting. They are attacked by a huge, snarling manbeast (Tyler Mane as Sabertooth) and then rescued by three mutants dressed in black leather. When Logan awakens, he is in a strange place looking into the face of a beautiful woman.
Rogue and Wolverine are now guests of Xavier, known to his students as Professor X. A powerful telepath, Xavier uses his own abilities, enhanced by a huge machine called Cerebro, to locate and bring young mutants to his academy. He warns Logan that Lehnsherr, who has incredible power over metal and calls himself Magneto, is looking for him and that he is in danger if he leaves the safety of the school.
If only it were that simple. Magneto has invented a device that magnifies his power and causes human DNA to mutate. He plans to use the device at an upcoming meeting of the heads of the world's powers, turning them into the very thing they fear most and, supposedly, heading off the attempts to control the mutant population. And it isn't Logan he wants, but Rogue, whose power enables her to absorb the life energy and, briefly, the mutant ability of anyone she touches. When he and his minions Sabertooth, Mystique (Rebecca Romijn-Stamos) and Toad (Ray Park) succeeds in abducting her, Logan the lone Wolverine must join Xavier's oldest students--Scott Summers (James Marsden), Jean Grey (Famke Janssen) and Ororo Munroe (Halle Berry)--to save her as one of the X-Men.