In 1944, teenaged Erik Lehnsherr is among the many Poles forced into concentration camps by the Nazis. Upon being separated from his mother, he reaches out and to everyone’s shock the camp gates bend toward him, until one of the guards knocks him out.
In “the not too distant future,” many more people have been born with mutant powers in the next step of human evolution, and suffer fear and mistrust from most regular humans. After a lifetime of seeing humanity’s worst, Erik has lost all faith that peaceful co-existence is possible and is preparing for a war with humanity, taking the name Magneto. He’s opposed by his former school friend Charles Xavier, who has tremendous telepathic abilities and still believes in making peace with humans.
Mississippi high schooler Marie “Rogue” D'Ancanto is jolted out of her normal life when her mutant power activates while she’s kissing her boyfriend, revealing that any physical contact with another person will drain their energy into her. She runs away to Canada where she stops in a bar and sees a cage fighter known only as Wolverine defeat several opponents without getting a scratch, revealing his healing power. He’s confronted by anti-mutant humans after the fights, and reveals he also has metal claws that can extend from his hands which scare them off.
Rogue stows away in Wolverine’s truck, and he shares that his real name is Logan, but nothing else. They’re attacked by the monstrous Sabretooth, a henchman of Magneto, who crashes the truck, but are saved by two other mutants, Ororo “Storm” Monroe who can control the weather, and Scott “Cyclops” Summers who shoots deadly beams from his eyes.
Wolverine wakes up to find himself in Xavier’s “School for the Gifted,” to the public simply a private school for advanced children, but in fact a haven for young mutants who can’t find acceptance anywhere else. Some of them, like Cyclops, Storm, and telekinetic Dr. Jean Grey, stay on as part of Xavier’s team the X-Men fighting for mutant rights. Xavier also reveals he knows Wolverine has spent fifteen years drifting around with no memory of his previous life, and promises to help him get answers if he’ll stay so they can figure out what Magneto wanted with him.
Magneto’s other henchmen, shapeshifter Mystique and super jumper Toad, kidnap Senator Robert Kelly, a rabidly anti-mutant politician who’s spearheading a law requiring mutant identities to be registered with the government. He activates a machine that transforms Kelly into a mutant, able to contort his body into any space, which he uses to escape his cell.
Jean runs an MRI of Wolverine and discovers his entire skeleton has been enhanced with the metal adamantium, which he could only survive due to his healing power. That night, he has a nightmare about the experiments done to him, and when he wakes up with Rogue standing before him, he accidentally stabs her through the chest with his claws. Rogue touches his face during her pained flailing, causing her to briefly take on his healing ability and survive.
Mystique infiltrates the school as Rogue’s classmate Bobby “Iceman” Drake, and tells her Xavier is angry with her and she should leave. Xavier finds her at a train station using the supercomputer Cerebro he created with Magneto, and as the team heads out to get her, Mystique uses Xavier’s face to access Cerebro herself. Wolverine convinces Rogue to return, but Magneto arrives and reveals it was actually Rogue he was after all along. His metal-controlling ability lets him easily deal with Wolverine, and he then takes control of all the guns of the policemen who have arrived to force the other X-Men to let him leave.
Back at the school, Wolverine is furious at Xavier’s mistake and is about to leave when Kelly appears at the door. Xavier reads his mind and learns about Magneto’s machine, which also nearly killed him, and they realize he intends to have Rogue take his powers and use the machine herself. Xavier uses Cerebro again, but Mystique's sabotage puts him in a coma, forcing Jean to use it despite the risk with her less skilled power. She discovers the machine will be activated at the Statue of Liberty to change all the world leaders who will be meeting nearby, and in the meantime Kelly dies due to the unstable forced mutation, making clear what will actually happen if Magneto succeeds.
The X-Men arrive at the Statue, where Mystique takes on Wolverine while Toad handles the others. Toad is ultimately dispatched by Storm with a lightning bolt, while Wolverine’s senses defeat Mystique’s attempt to fool him with a disguise as Storm and he stabs her in the stomach. But then Magneto arrives and easily imprisons everyone, including pointing Wolverine’s hands at his own chest. After he leaves to give Rogue his powers, Wolverine stabs himself to break free, and upon healing has a vicious fight with Sabretooth until Jean is able to direct Cyclops’ visor to blast Sabretooth away. Storm and Jean then work together to fly Wolverine to Magneto, and with him distracted controlling Wolverine, Cyclops shoots him too. Rogue is left dying, so Wolverine has her again take his power and she heals. The police arrive and Magneto is arrested, while Mystique manages to disguise herself as another cop to get taken to the hospital.
Xavier wakes up and presents Wolverine with an abandoned military base in the Canadian Rockies where he may get answers to his identity. As Wolverine heads out, the others see a news report that Mystique is now posing as Kelly, starting by killing his registration law. Xavier then visits Magneto, who is being held in a special cell made entirely of plastic that he can’t control. Magneto insists the war with humanity is still coming, to which Xavier retorts "And I will always be there, old friend."
