The scene opens in a Nazi concentration camp during World War II in Poland, 1944. A young boy is forcefully taken from his parents. Frightened, he tries to reach out to them. At this time, his mutant powers manifest and he bends the metal gates open towards him. The guards knock him out by striking his head with a rifle.
In Meridian, Mississippi, a young girl named Marie manifests her mutant powers while kissing a boy, sucking his life force from him and putting him in a coma. Frightened, she runs away from home.
In Washington D.C., Dr Jean Grey addresses the Senate regarding the Mutant Registration Act. She is “urging the Senate to vote against mutation registration”. Unfortunately, Senator Kelly, the vocal activist of the Mutant Registration Act, has won over the public audience by playing on their fear of how “dangerous” mutants can be.
Professor Charles Xavier spots his long time friend, Erik Lensherr in the Senate crowd. He follows Erik outside. Charles urges Erik to give up on the hope of a peaceful co-existence between humans and mutants. But Erik insists that a war is brewing, and he asks Charles not to “get in [his] way”.
Marie finds herself in Northern Alberta, Canada. On the road, she adopts the name, Rogue. She watches a cage fight take place. A man named “Wolverine”has apparently won every fight of the night. Later, she sits by the bar, eyeing the jar of tips, which the bartender promptly removes from her reach. Wolverine joins her at the bar. The man he last fought seeks revenge, and threatens to expose Wolverine being a mutant. A fight breaks out, and Wolverine reveals his metal claws. Not wanting to cause trouble, he leaves. Rogue stows away in his vehicle.
Not long after, Wolverine finds Rogue. He tosses her out of his vehicle, but with a change of heart, he lets her back in the car. Rogue tries to make small talk but she seems to be hitting all his nerves. After a few stumbles, she at least manages to get his name: Logan. Suddenly, the vehicle crashes into a fallen tree. Logan is flung out through the windscreen and onto the road. His rapid healing shocks Rogue. Just then, Sabretooth attacks Logan, knocking him out. A fire starts in the vehicle, but Rogue’s seatbelt is stuck. Two people in black leather suits, Cyclops and Storm, drive Sabretooth away, and gets Logan and Rogue to safety.
On a remote island, Erik, now also known as Magneto, is angry that Sabretooth didn’t get the job done.
Logan awakens in a medical laboratory. Dr Jean Grey attends to him. He attacks her, but briefly lets her go and escapes into the hallway. He wonders around the mysterious mansion with children running around, with a voice in his head. He stumbles into a room, interrupting a Physics class taught by Professor Charles Xavier. Logan stares in disbelief as he watches a girl, named Kitty, disappear through the closed doors after her classmates. Xavier introduces himself and his “School for the Gifted”, as well as his staff, Ororo Munroe (Storm), Scott Summers (Cyclops) and Jean Grey. Xavier also warns Logan about Magneto and Sabretooth who tried to hurt, and possibly apprehend him. Logan is amused and dumbfounded. To help Logan understand better, Xavier gives him a private tour of the school.
Xavier explains that he created this school to protect and teach mutants how to control their powers. Scott, Jean and Ororo were “one of [his] first students”, and now, they help their mentor, Xavier, teach others “to do the same”. Logan watches Rogue attend Ororo’s history class, and Scott teach shop class, with Jean seated next to him. The latter two hold hands. Xavier reveals a jet hidden in the “lower levels”. They are also a team of mutant vigilantes, known to the student population as the “X-Men”.
Senator Kelly is abducted by Mystique and Toad. Magneto intends to experiment his machine on Kelly, which would turn him into a mutant.
Back in the medical laboratory, Jean goes a full body scan on Logan. His entire skeleton is grafted in adamantium. Coupled with his healing powers, Logan is quite invulnerable. His age is also “impossible to determine”. Jean has a discussion with Xavier, Scott and Ororo. Thinking back to the attack, Xavier isn’t positive that Magneto is interested in Logan.
Jean shows Logan to his sleeping quarters. Logan tries to flirt with her, but Jean promptly informs him that she is engaged. When asked about her mutant powers, she replies she is both telekinetic and telepathic. Logan asks her to read his mind. Jean sees deep into his past for a moment, before Scott interrupts them. Jean takes her leave. Scott and Logan lock horns, and Scott leaves Logan to retire for the night.
Unable to sleep, Rogue goes to find Logan. Logan jolts from his nightmares, and accidentally stabs Rogue. Rogue draws his healing powers to save herself, creating a minor commotion. The students are alerted by her screams, as well as the adults. As the resident physician, Jean promptly tends to Logan, with Scott aiding her.
Kelly’s mutation is a success. With his ability to contort himself, he squeezes out of the window of his cell. Sabretooth tries to pull him up, but Kelly falls into the sea below. He washes up on the beach, with everyone staring at him.
Rogue sits by herself in the gardens. Bobby Drake comes over to talk to her. Bobby tells her “the students are freaked”, “Professor Xavier is furious” and that she “should go”. Rogue takes off, and Bobby reveals himself to be Mystique in disguise.
Xavier is re-examining Logan’s scans with Scott. Scott makes no qualm in expressing his dislike for Logan. Logan interrupts Xavier, alerting him of Rogue’s disappearance. Xavier introduces Logan to Cerebro, a machine designed to enhance Xavier’s powers and help him locate mutants. Logan asks Jean if she’s ever used Cerebro. She replies no. Scott adds that it would be “dangerous” for her. Xavier emerges after a few minutes, with news that Rogue is at the train station.
Logan ignores Xavier’s warnings to stay within the mansion. He takes off on Scott’s motorcycle. Scott and Ororo head for the train station as well. At the station, Logan finds Rogue on a train, and tries to talk her into going back to the mansion, where Xavier would be best able to help her.
With the mansion unguarded, Mystique proceeds to sabotage Cerebro.
Ororo goes to “check with the ticket agent” regarding Rogue while Scott looks around for her. Ororo is attacked by Sabretooth. As Scott goes to help her, Toad grabs Scott’s visor, causing Scott to bore a hole through the roof with his optic blasts. Ororo uses lightning to strike Sabretooth, flinging him into a wall.
Magneto halts the moving train with his powers and promptly abducts Rogue. With Sabretooth and Toad in tow, he leaves the station with Rogue. The police arrive at the station, but their metal guns prove no match against the power of Magneto. Jean drives Xavier into the parking lot, where Xavier places Sabretooth and Toad under his telepathic control. He uses Sabretooth to physically threaten Magneto, and controls Toad to bring Rogue towards him. Magneto fires a gun at an officer, the bullet stopping short of penetrating the latter’s forehead. “Unwilling to make sacrifices”, Xavier releases his control, allowing Magneto to leave in a helicopter.
Logan is angry with Xavier and the X-Men, and is determined to look for Rogue himself. As he is about to leave, Senator Kelly collapses in his arms at the main door, looking for Dr Jean Grey. Xavier probes Kelly’s mind and sees how Magneto mutated Kelly. The artificial radiation causes mutation in normal humans, but Kelly’s body is “rejecting” the transformation. Piecing bits of information together, they figure out Magneto’s intentions with Rogue. Xavier wants Logan to join the team, but Scott disapproves. Ororo runs in to inform them of Kelly’s death. Xavier tells both men to settle their differences while he uses Cerebro to find Rogue.
Xavier is poisoned by the sabotaged Cerebro. Scott keeps virgil by Xavier’s side. Jean fixes Cerebro, and on second thought, attempts to use Cerebro. Scott tries to stop her but is too late as Jean activates Cerebro. Strained, Jean finds out where Rogue is, allowing the team to go forth in completing the mission. After a quick briefing and suiting up, they leave in the jet. The students stare in awe as the jet rises from beneath the basketball courts.
Upon landing, the X-Men head straight for the statue’s torch. They are attacked by Mystique, who takes on Wolverine, and Toad. Toad takes out Cyclops quickly, and works on Storm and Jean. He slimes Jean in the face, and tosses Storm into the elevator shaft. Regaining consciousness, Cyclops quickly removes the slime from Jean’s face. Storm emerges from the shaft, striking Toad with lightning. Wolverine surprises and stabs Mystique, taking her out.
As they make their way up to the torch, Magneto uses strips of metal to pin the X-Men to the sides of the inside of the torch. Jean and Storm try to talk Magneto out of his intentions, telling him he will kill the world leaders if he did mutate them. But Magneto proceeds with the mutation anyway. Wolverine cuts himself out of the metal strips, and battles Sabretooth atop the statue. Tossing Wolverine over the head and thinking he’s been taken care of, Sabretooth goes back inside the head. Wolverine tosses Jean Cyclops’ visor. Jean telekinetically catches and configures Cyclops’ visor, and Cyclops blasts Sabretooth out of the head.
The X-Men have to make quick decisions to stop Magneto before it is too late. Wolverine volunteers to be flown up to the torch by Storm’s winds to stop. Despite being weakened, Magneto reaches out in desperation to stop Wolverine. Cyclops’ blast stuns Magneto and Wolverine is able to destroy the machine. Wolverine’s healing powers revive an unconscious Rogue, but severely weakens him. Regrouping, the X-Men retreat, and leave Magneto and his people to the authorities. There aren’t traces of Sabretooth and Toad, but Mystique gets away by disguising herself as an injured security officer.
Xavier awakens and Logan is fully healed. Jean tries to confront him on his feelings towards her, but he quickly changes the subject to inquiring about Xavier. Later, Xavier tells Logan of his findings: an “abandoned mine” at Alkali Lake. Logan takes off on Scott’s motorcycle after saying goodbye to Rogue, reassuring her that he’ll be back for his dogtags he had given her.
Scott, Jean and Ororo watches as Mystique impersonates Senator Kelly on television, addressing the public on his decision to step down regarding the Mutant Registration Act.
Xavier visits Erik in the latter’s plastic prison. Erik tells Xavier he’ll continue to fight the war. Xavier replies he’ll be there to make sure the war doesn’t happen.
Next: X2: X-Men United