In Nazi-occupied Poland, in 1944, young Erik Lehnsherr is separated from his parents upon entrance into the Auschwitz concentration camp. While he attempts to reach them, he causes a set of metal gates to bend toward him. This the result of a mutant ability to create magnetic fields and control metal manifesting, but he is knocked out by the guards. In the not too distant future, U.S. Senator Robert Kelly attempts to pass a “Mutant Registration Act” in Congress, which would force mutants to reveal their identities and abilities. Present are Lehnsherr, now going by the name “Magneto”, and his telepathic colleague Professor Charles Xavier. Xavier sees Lehnsherr in attendance and is concerned with how he will respond to the Registration Act.
In Meridian, Mississippi, 17-year-old Marie D’Ancanto accidentally puts her boyfriend into a coma after she kisses him, because her mutant ability absorbs the power and life force of others. She runs away from home and adopts the name Rogue. In Alberta, she meets Logan, also known as Wolverine, a mutant who possesses superhuman healing abilities and metal “claws” that protrude from between his knuckles. They are attacked on the road by Sabretooth, one of Magneto’s minions, but two of Xavier’s teachers – Cyclops and Storm – arrive and save them. Wolverine and Rogue are brought to Xavier’s mansion and school for mutants in Westchester County, New York.
Xavier tells Logan that Magneto appears to have taken an interest in him and asks him to stay while Xavier’s mutants, the X-Men, investigate the matter. Rogue enrolls in the school.
Senator Kelly is abducted by two more of Magneto’s minions, Toad and Mystique, and brought to 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. Kelly later escapes by taking advantage of his newfound mutation.
Rogue visits Wolverine during the night while he is having a nightmare. Startled, he accidentally stabs her, but she’s able to absorb his healing ability to recover. This is observed by fellow students who arrived to help. She is later convinced by Mystique, who disguises herself as Rogue’s crush Bobby Drake, that Xavier is angry with her and she should leave the school. Xavier uses his mutant-locating machine Cerebro to find Rogue at a train station, and the X-Men go to retrieve her. Meanwhile, Mystique enters Cerebro and sabotages it.
Having left ahead of Storm and Cyclops, Wolverine finds Rogue on a train and convinces her to return to the school. Before they can leave, Magneto arrives, knocks out Wolverine and subdues Rogue, revealing it was Rogue who he wants rather than Wolverine. Although Xavier attempts to stop Magneto by mentally controlling Sabretooth, he is forced to release his hold on Sabretooth when Magneto threatens the police who have converged on the train station, allowing Magneto’s Brotherhood to escape with Rogue. Kelly arrives at Xavier’s school, and Xavier reads his mind to learn about Magneto’s machine. Realizing the strain of powering it nearly killed Magneto, the group deduces 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. Xavier attempts to locate Rogue using Cerebro, but Mystique’s sabotage incapacitates him, and he falls into a coma. Fellow telekinetic and telepath Jean Grey fixes Cerebro and uses it, learning that Magneto plans to place his mutation-inducing machine on Liberty Island and use it to “mutate” the world leaders meeting at a summit on nearby Ellis Island. The X-Men scale the Statue of Liberty, battling and overpowering the Brotherhood while Magneto transfers his powers to Rogue and activates the mutating machine. As Wolverine confronts and distracts Magneto, Cyclops blasts him away, allowing Wolverine to destroy the machine. He transfers his powers to Rogue and his healing abilities rejuvenate her, while incapacitating himself.
Professor Xavier and Wolverine recover from their comas. The group also learns that Mystique escaped the island battle and is impersonating Senator Kelly. Xavier gives Wolverine a lead to his past at an abandoned military installation in Canada. Magneto is imprisoned in a complex constructed of plastic and is visited by Xavier, and Magneto warns him he intends to escape one day and continue the fight.