प्लॉट

In 1944 German-occupied Poland, a 13-year-old boy is separated from his parents upon entry to a concentration camp. The parents are taken into the concentration camp, but the boy is kept outside as the kids are to be taken to a different section of the camp. When he tries to get back in after the gates have been closed, he is restrained by four guards. The gates suddenly start to curl in towards the group, as though attracted by a magnetic force; the boy is then knocked unconscious by another guard.

In present day, a 17-year-old girl named Marie (Anna Paquin) is studying with her boyfriend at her house in Meridian, Mississippi. They hug and kiss, which knocks him out and he almost dies, because of her mutant ability to absorb the power and life force of others. She screams as her mother arrives. Terrified, she doesn't allow anyone to touch her and decides to leave her home.

In Congress, Senator Robert Kelly (Bruce Davison) attempts to pass a "Mutant Registration Act", which would force mutants to publicly reveal their identities and abilities. The mutations are triggered at puberty, under conditions of heightened emotional stress. Kelly says that mutants have the ability to walk through walls, and some can even control the minds of other humans.

Nearby, telepathic mutant Charles Xavier sees Lehnsherr, who now goes by the name "Magneto", in attendance and is concerned with how he will respond to the Registration Act. Magneto (Ian Mckellan) begins his plans to level the playing field between mutants and humans.

Meanwhile, Marie (aka Rogue) meets Logan (aka Wolverine (Hugh Jackman) at the local bar in Canada. Rogue's mutation makes her temporarily assume the powers of any mutant she touches, while Wolverine possesses superhuman healing abilities, heightened senses, and metal claws that extend outwards from his knuckles.

Suddenly, both of them are attacked by Sabretooth (Tyler Mane), a mutant, an associate of Magneto. Cyclops (James Marsden) and Storm (Halle Berry) arrive and save Wolverine and Rogue and bring them to the X-Mansion in Westchester County, New York. Professor Charles Xavier (Patrick Stewart) runs the facility and leads a group of mutants who are trying to seek peace with the human race, educate young mutants in the responsible use of their powers, and stop Magneto from starting a war with humanity. Believing that Magneto is interested in capturing Logan, Xavier asks him to stay while he investigates the matter. Meanwhile, Rogue enrolls in the school as a new pupil and develops a crush on Cryokinetic mutant Bobby Drake/Iceman (Shawn Ashmore).

Abducted by Mystique (Rebecca Romijn-Stamos) and Toad (Ray Park) Senator Kelly is brought to Magneto at their hideout on the uncharted island of Genosha. Magneto uses Kelly as a test subject for a machine powered by his magnetic abilities that generates a field of radiation, which induces mutations in normal humans. Though Kelly manages to escape imprisonment with his new abilities.

Rogue visits Logan during the night while he is having a nightmare. Startled, he accidentally stabs her, but she manages to absorb his healing ability and recover. Rogue is convinced by Mystique (disguised as fellow-school-mate Bobby Drake) that Xavier is angry with her and that she should leave the school.

Having left ahead of Storm and Cyclops, Logan finds Rogue on a train and convinces her to return. Before they can leave, Magneto arrives, incapacitates Logan and subdues Rogue, revealing it was her whom he wants rather than Logan. Although Xavier attempts to stop him by mentally controlling Sabretooth, he is forced to release his hold when Magneto threatens the police who have converged on the station, allowing the Brotherhood to escape with Rogue.

Kelly arrives at the school, and Xavier reads his mind to learn about Magneto's machine. Realizing the strain of powering it nearly killed him, the X-Men deduce he intends to transfer his powers to Rogue and use her to power it at the cost of her life. Kelly's body rejects his mutation, and his body dissolves into liquid.

The X-Men learn that Magneto was severely weakened in the test of the machine on Kelly, and Wolverine realizes he intends to use Rogue's ability to transfer his powers to her, so that she can power his machine in his place, possibly putting her life at risk. Xavier attempts to use Cerebro to locate Rogue, but falls into a coma, due to Mystique's earlier meddling with the device.

Jean Grey (Famke Janssen) fixes it and uses Cerebro to find Magneto's machine on Liberty Island, which Magneto intends to use on the world leaders, who are meeting for a summit on nearby Ellis Island. Just as the group arrives at the top of the statue, defeating Toad and incapacitating Mystique, Magneto and Sabretooth incapacitate the group and continue with their plans. Magneto transfers his powers to Rogue (which makes part of her hair go white), who is forced to use them to start the machine. Wolverine breaks free and initiates a fight with Sabretooth but is thrown off the top of the statue.

Wolverine returns, and Cyclops, with Jean's help, blasts Sabretooth out of the statue. With Jean's telekinesis stabilizing him, Storm uses her abilities to send Wolverine to the top of Magneto's machine. With time running out, Wolverine attempts to stop the machine and save Rogue, but Magneto, now having regained some of his strength, halts Wolverine's claws. Cyclops manages to find a clean shot, wounding Magneto and allowing Wolverine to destroy the machine. Placing his hand to Rogue's face, as she is dying, Wolverine succeeds in transferring his regenerative abilities to her; Professor Xavier also recovers from his coma. The group learns, after seeing Mystique impersonating Senator Kelly on a news broadcast, that, despite being stabbed by Wolverine at Liberty Island, she is still alive.

In an attempt to help him learn more about his past, Xavier sends Wolverine to a military base near Alkali Lake. Xavier visits Magneto in his plastic prison cell, and the two play chess. Magneto warns his friend that he will continue his fight, to which Xavier promises that he (and the X-Men) will always be there to stop him.