In a world where mutants (evolved super-powered humans) exist and are discriminated against, two groups form for an inevitable clash: the supremacist Brotherhood, and the pacifist X-Men.
In a world where both Mutants and Humans fear each other, Marie, better known as Rogue, runs away from home and hitches a ride with another mutant, known as Logan, a.k.a. Wolverine. Professor Charles Xavier, who owns a school for young mutants, sends Storm and Cyclops to bring them back before it is too late. Magneto, who believes a war is approaching, has an evil plan in mind, and needs young Rogue to help him.
Born with extraordinary abilities in a world filled with fear, prejudice, and intolerance, the next link in the chain of human evolution, the powerful meta-humans, will soon have to choose sides. As the telepathic mutant, Professor Charles Xavier, struggles to achieve a peaceful coexistence between the two species, hoping that the gifted students of his institute will use their powers for good, his old friend and super-human antagonist, Magneto, prepares for war. Now, Professor X's newest students--the teenage mutant with the deadly touch, Rogue, and the body-regenerating, adamantium-infused Logan, aka Wolverine--find themselves caught in the middle of a violent confrontation; one that would either stop or usher in a new era in the history of homo superior. Can Xavier's X-Men put an end to Magneto's megalomaniac vision?
In the near future, when children are being born with a special X-factor in their genes, giving them special powers and making them mutants, the seeds of a new Holocaust are being sown by Senator Robert Kelly. The situation brings into opposition the fellow mutants and former friends, Erik Lehnsherr, a.k.a. Magneto, and Professor Charles Xavier. While Xavier wants a peaceful means of stopping the hatred toward mutants, Magneto seeks to even things out with a machine that would speed up the mutation process in all humans, making everyone equal. To stop Magneto, Xavier brings together a special group of mutants called "X-Men" to stop him. In the meantime, two mysterious mutants emerge: Logan, a powerful and aggressive mutant with no past, no memories, and a young girl named Rogue. Their quests for identities eventually land them in the sights of Xavier and Magneto, but for what purpose?
After the death of his family at the hands of the Nazis, Magnus, a mutant, vows revenge on all humanity. Meanwhile, a group of good mutants is assembled by Professor Charles Xavier, who trains and cares for them. Magnus, now under the guise of Magneto, assembles the villains Sabertooth and Mystique to destroy anyone who gets in his way, including a furry Canadian mutant named Logan (Wolverine). A fierce battle ensues between Sabertooth and Wolverine. Xavier's group, the X-Men, recruits Logan just in time to learn of Magneto's dastardly plan to destroy the world.
Across the world, children are born with an extra twist to their chromosomes that allow them to exhibit superhuman abilities: fire a beam of force from their eyes, sprout wings that allow flight, or read people's minds. These "children of the atom" are often feared and despised by the world, forcing these mutants to resort to desperate actions. However, one group of mutants have banded together to show the world that it need not fear their kind. Apart, they are simply scientific curiosities, freaks, and monsters, but together, united by their shared belief, they are more. They are the uncanny X-Men.
- Evolution of some lifeform to another is a slow process which takes thousands of years, but every few hundred millennia, some abrupt change may happen giving rise to what is called mutants with special properties and powers. In a world where both humans and mutants are living, a group of mutants that seeks peace and friendship with humans, is led by Professor Charles Xavier who has ability to control others' thoughts and actions; and his students Dr Jean Grey who has telepathic and telekinetic abilities; Cyclops who has the ability to fire an optic blast from his eyes; and Storm who has ability to create storm and lightning. Another group of mutants comprise Sabretooth who features a sabre-tooth, Toad who features a frog like tongue, and Mystique who is a shape-shifter. They are led by Magneto who harbors deep hatred for human race due to his tragic past as a boy Eric in Nazi ruled Poland and now has the ability to create magnetic field.
In US Congress, Senator Robert Kelly attempts to pass a "Mutant Registration Act", which would force mutants to publicly reveal their identities and abilities. Magneto begins his plans to fight against humans. Meanwhile, a mutant girl named Marie (a.k.a Rogue) discovers that the touch of her skin physically hurts that person by absorbing their energy/powers and runs away from her home in Mississippi. In Canada, she meets another mutant Wolverine (a.k.a. Logan) who has quick healing power and retractable metallic claws which he brings out from inside his body when threatened. After a fight, Logan drives away in his truck and gives Rogue a lift. Suddenly, both of them are attacked by Sabretooth. Cyclops & Storm arrive and save Logan & Rogue and bring them to Prof Xavier's mansion. Prof Xavier reveals to Logan that he runs the facility in the disguise of a school where they educate young mutants in the responsible use of their powers, who may either rejoin the human society or stay there as "X-Men". Below the surface, they aim to stop Magneto from starting a war with humanity. Rogue joins the school and likes a boy named Bobby Drake there.
Senator Kelly, the face of anti-mutant public demonstrations, is abducted by Mystique & Toad and taken to Magneto. Magneto runs a machine that emits a radiation on Kelly and artificially induces mutation, though Kelly manages to escape imprisonment with his new abilities. After an accident causes Rogue to absorb Logan's powers, she is convinced by Mystique (disguised as Bobby) that others are now afraid of her and she should leave the school. Xavier has a machine called Cerebro to locate the mutants around and he uses that to locate the fleeing Rogue at a train station. Mystique infiltrates Cerebro and sabotages the machine. Logan grabs a bike to reach the train station and convinces Rogue to stay with Xavier. Cyclops and Storm too reach the station searching for her but a fight ensues when Magneto, Toad and Sabretooth arrive and they take Rogue. Kelly, now a new mutant, seeks help of Dr Grey at Xavier's school to cure him, but he dissolves into a puddle of water when his mutation becomes unstable.
Magneto brings Rogue to Liberty Island and places his machine atop the Statue of Liberty. He intends to use his machine on the world leaders who are meeting for a UN summit on nearby Ellis Island and change them into mutants. The X-Men learn that the machine draws its energy from Magneto and thus weakened him in previous use, to the point of nearly killing him, so he has abducted Rogue who can be used to absorb his powers and then be used to start his machine. Xavier attempts to use Cerebro to locate Rogue but the compromised machine sends him into a coma. Jean fixes it and locates Rogue on Liberty Island. Logan, Jean, Cyclops and Storm take a jet to arrive at the top of the statue and a fight ensues with Mystique disguised as Logan. Toad is killed by Storm's lightning and Mystique is apparently killed by Logan, but then Magneto incapacitates the group with his magnetic powers. The X-men tell Magneto that Kelly is dead and his machine is a killer, not converter. However Magneto goes ahead with his plan arguing it to be fair. Magneto transfers his powers to Rogue who is forced to sit inside the machine and then start it. Logan breaks free and initiates a fight with Sabretooth. Cyclops, with Jean's help, blasts his optic rays on Sabretooth smashing him out of the statue. With Jean stabilizing him, Storm creates a storm to propel Logan to the top of Magneto's machine. With time running out, Logan attempts to stop the machine and save Rogue, but Magneto, now having regained some of his strength, halts Logan's claws. Cyclops manages to find a clean shot, wounding Magneto and allowing Logan to destroy the machine and the radiation stops short of reaching the people.
Placing his hand to her face, Logan succeeds in transferring his regenerative abilities to a dying Rogue who recovers. Magneto is arrested. Professor Xavier recovers from his coma and the group finds that Mystique is still alive, now impersonating Senator Kelly. In an attempt to help Logan learn more about his past, Xavier sends him to a military base near Alkali Lake. Xavier visits Magneto in his prison, who warns that he will continue his war, to which Xavier promises that he (and the X-Men) will always be there to stop him.