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Terrified by powers that prevent her from touching anyone, teenager Marie runs away from home and is reluctantly picked up by drifter Logan, who she meets in a bar. The pair are attacked by another mutant and during the fight Logan reveals his own mutation, sharp retractable claws and a healing ability. The X-Men arrive just in time to save the pair and take them with them to Xavier's School in Westchester New York. The school is a front for Xavier's team of super powered mutants, the X-Men, who train young mutants to use their powers and combat threats super-villain Magneto. Xavier believes in harmony between humans and mutants while his old friend and nemesis Magneto believes in mutant supremacy.

Magneto's latest plot involves the kidnapping of Senator Kelly, an outspoken opponent of mutants who supports a Mutant Registration Act. They test out a machine developed by Magneto on the senator, giving him a mutation. Kelly escapes but can't control his mutation and transforms into water just as he reaches the X-Mansion in search of help. At Xavier's school, Rogue accidentally uses her powers to absorb Logan's. Magneto's shape-shifting cohort turns into a friend of Rogue's and convinces her that everyone at the school hates is mad about mistake. Rogue runs away from the school.

Logan finds Rogue but Magneto's henchman arrive and she's kidnapped during the ensuing battle. Magneto needs her to absorb his abilities to power his mutant power granting machine. The X-Men confront him on Liberty Island where plans to use his machine to change a meeting of world leaders into mutants. Magneto overpowers the X-Men and starts his machine. The X-Men regroup and attack, this time stopping Magneto and his machine. Logan saves Rogue's life by giving her his healing power. Xavier meets up with Magneto later and they make it clear to one another that their fight is not over.