1944, In a polish prison camp, a young Eric Lensherr is separated from his parents. Suddenly, the barbed wire fence is being pulled towards the soldiers as a frightened Lensherr manifested his mutant powers.
1988, In Kenya, Africa, a group of tribal children taunt and tease a little girl with white hair. Suddenly, chunks of ice fall from the sky over the children, except the little girl, who would eventually learn to control the weather with her powers.
One year ago at a high school dance in Mississippi, a girl sucks the life out of her boyfriend and lands him in a coma just by kissing him.
A senate hearing is held in Washington D.C. at present. “Mutant expert” Dr Jean Grey “testifies before Senator Robert Kelly’s subcommittee”. In her presentation, Dr Grey explains that 80% of the current genes are unused, referred to as “junk D.N.A.”. With mutation, the “junk D.N.A.” became a “storehouse of almost limitless potential for human advancement”. She encourages the Senate to understand mutants, rather than discriminate them. But Senator Kelly plays on human’s fear of mutants and convinces the committee that mutants are dangerous and the Mutant Registration Act should be passed. He threatens Dr Grey with a folder of evidence that mutants are dangerous, and when he refuses to let her have a look at the folder, she snatches it from him with her telekinesis.
Professor Charles Xavier, present for the hearing, spots Eric Lensherr in the crowd leaving the hearing. Lensherr is certain that the committee will pass the Mutant Registration Act despite efforts to persuade the Senate otherwise. Xavier urges Lensherr to have faith in the Senate. But Lensherr is insistent that a war is brewing.
In Alberta, Canda, a man named Logan walks into the Lion’s Den with a photograph in hand. The photograph pictures him with a woman, possibly a loved one. He meets a girl (who had put her boyfriend in a coma the previous year) being harassed by a group of thugs. Logan makes short work driving the thugs away, revealing himself to be a mutant. The girl, who calls herself Rogue, takes off with him.
After driving a short distance, Logan’s vehicle crashes and he is flung out of the windscreen because he wasn’t wearing his seat belt. He is then attacked by a mutant named Sabretooth. Rogue is stuck in the vehicle that has now caught fire. Logan and Rogue are rescued by two people in black leather suits, named Cyclops and Storm.
Sabretooth, who is working for Lensherr, also known as Magneto, returns to Magneto’s lair without completing the task he was sent to do. Magneto starts working on another plan.
Logan and Rogue are brought to the Xavier School for Gifted Youngsters. Logan is being medically examined by Dr Grey. Awakened, he promptly attacks her and escapes the medical laboratory, only to run into Xavier. Xavier explains to Logan that Magneto attacked him and Rogue. Logan would be safe here while Xavier tries to figure out Magneto’s plans.
Scott Summers (field name Cyclops) comes bursting into the room thinking Xavier needed protection after Scott’s fiancée Jean, got attacked by Logan. After assuring Scott that he is fine, Xavier makes brief introductions. Impatient, Logan wants to take off. Xavier makes Logan an offer: To convince Logan to stay out of Magneto’s reach for 48 hours, Xavier has promised Logan to help try to piece his past together and “find what [he’s] looking for”. Logan apologises to Jean and makes a pass at her, angering Scott.
Meanwhile, Magneto has Mystique capture Senator Kelly. Magneto has plans to mutate Kelly using a special machine powered by Magneto’s powers. After the mutation is supposedly complete, Magneto lets Kelly go.
That night, Rogue hears Logan’s screams and tries to wake him from his nightmare. She gets stabbed instead, but uses her ability to absorb other mutant’s powers, in this case Logan’s healing factor, to heal herself. Scott, Jean and Ororo (field name Storm) come running in and witness Rogue’s powers in action. She leaves after healing herself. Jean immediately goes to check on Logan’s weakened condition, angering Scott even more to see Jean showing what he deems affection towards Logan.
The next morning, a student named John comes to talk to a distraught Rogue. He tells her that Xavier is angry that she “used [her] power against another mutant”. He tells her it is best for her to leave. Rogue is unaware that John is actually Mystique in disguise.
Xavier uses Cerebro to locate Rogue who had run away from the mansion. He finds her at the train station. Logan takes off and finds Rogue on the train. He tells Rogue that she should go back to the mansion as Xavier would be able to help her with her powers. The train comes screeching to a halt as Magneto attacks and captures Rogue. Cyclops and Storm are kept busy being attacked by Sabretooth and Toad.
With no one to guard the mansion, Mystique proceeds to sabotage Cerebro using her disguise as Xavier to gain entry.
Outside the train station, Xavier controls the minds of Sabretooth and Toad, physically threatening Magneto to let Rogue go. Gaining control of the police’s guns, Magneto pulls the trigger on a police officer, the bullet stopping short of penetrating the officer’s head. Refusing to shed blood, Xavier releases Magneto. He takes off in a helicopter piloted by Mystique.
Back in the mansion, Logan and Scott get into a fight after Scott tries to stop Logan from attacking Xavier. Angry, Logan takes off to find Rogue himself. At the front door, a mutated Senator Kelly collapses in Logan’s arms.
Xavier probes Kelly’s mind and learns of Magneto’s machine and the latter’s plans. Kelly dies not long after. Fearing Magneto was going to use Rogue to “amplify” his powers, Xavier uses Cerebro to try to locate Rogue immediately. The sabotaged Cerebro leaves Xavier in a comatose state. Scott and Ororo tend to Xavier while Jean fixes Cerebro and locates Rogue. Cyclops, Storm, Jean and Logan suit up and head for Liberty Island.
Upon entering the Statue of Liberty, Logan is attacked by Mystique disguised as him. Toad makes short work of taking out Cyclops, Storm, and slimes Jean in the face. Scott tends to Jean while and angry Storm tosses Toad out of the statue and into the waters below. Logan finally knocks Mystique out, and the four make their way to the head of the statue. They are ambushed by Magneto and are held against the wall by metal strips.
Logan breaks free and starts attacking Sabretooth as Magneto puts his ultimate plans in action, transferring his powers to Rogue to power his machine. After joint efforts to take out Sabretooth, Logan tells Storm to lift him up to the torch with her winds so he can destroy Magneto’s machine and take Magneto out. He rushes to tend to Rogue, allowing her to absorb his healing factor.
After Logan has recovered, Xavier tells Logan that he has found “an abandoned military compound at Alkali Lake in the Canadian Rockies” and that it might provide some answers. Logan leaves for Alkali Lake on a bike that Scott loaned to him. In a turn of good news, the Senate committee voted against the Mutant Registration Act.
Xavier pays a visit to his old friend, Lensherr, in the latter’s plastic prison. Lensherr tells Xavier not to stand in his way of the war. Xavier replies that he will always “be there to oppose [him]”.