The X-Men (Cyclops, Jean Grey, Rogue, Wolverine, and Storm) stop Magneto from turning the world's population into mutants. Wolverine then drives off on Cyclops' motorcycle (without permission) in search of the answers to his past.
The villainous Magneto (Ian McKellen), a Holocaust survivor, has assembled a band of mutants (Toad (Ray Park), Mystique (Rebecca Romijn), and Sabertooth (Tyler Mane)) to aid him in his cause to establish mutant dominance in the world. Meanwhile, Wolverine (Hugh Jackman) and Rogue (Anna Paquin) are recruited by the X-Men, who live with Professor Charles Xavier (Patrick Stewart), the X-Men's leader and the headmaster of the Xavier's School for Gifted (i.e. Mutant) Children. The X-Men are a group of adult mutants who oppose evil mutants. The goal of Professor Xavier and the X-Men are to teach young mutants how to use their powers responsibly and to foster peace between mutants and humans. Professor Xavier and Magneto were once friends, but due to their differing philosophies on the role of mutants, they have become enemies. Meanwhile, Senator Kelly (Bruce Davison) is seeking to pass a bill that would require all mutants to register themselves to the government.
The X Men are comprised of Storm (Halle Berry), Jean Grey (Famke Janssen) and the leader Cyclops (James Marsden). They eventually convince Wolverine to join them. Although Wolverine has the hots for Jean Grey, she is dating Cyclops, leading to tension between the three. Meanwhile, Rogue joins the school and befriends various other mutants, notably Iceman (Shawn Ashmore) and Pyro (Alex Burton). Rogue's powers cause her to temporarily absorb and amplify the powers and lifeforce of any being she has skin-to-skin contact with. Senator Kelly is kidnapped by Magneto, who uses a machine to turn Senator Kelly into a mutant. The machine ends up draining almost all of Magneto's powers, and it ends up killing Senator Kelly (albeit, after he is rescued by the X-Men and admits the error of his ways). Magneto's mutants infiltrate Xavier's school, put Xavier in a coma, and abduct Rogue. The X-Men follow in hot pursuit, but are defeated by Magneto's minions. It turns out that Magneto intends to have Rogue absorb and amplify his powers so that he can use his machine to convert the entirety of the world into mutants.
The X-Men escape, with Wolverine defeating both Sabretooth and Mystique, and Storm defeating Toad. They then work together to defeat Magneto and destroy his machine. Professor Xavier comes out of his coma, and the X-Men have saved the day. Mystique, having survived the battle, ends up impersonating Senator Kelly and leads the charge against the registration act. Wolverine takes off to find answers about his past (Wolverine suffers from amnesia), and takes Cyclops' motorcycle to tweak him. Meanwhile, Professor X visits Magneto who is being held in a plastic cell. As they play chess, Magneto swears to escape and try again, and Professor X vows that he and the X-Men will be waiting for him.