In a concentration camp in World War II, a boy named Erik Lehnsherr is tortured by a Nazi scientist Dr. Schmidt as Schmidt tries to coerce the boy into using his strange powers over magnetism. Schmidt kills Erik's mother and it is only because of his powers that the boy is allowed to live. Across the globe in Westchester New York another boy, Charles Xavier, reveals his powers of telepathy when he meets a shape shifting girl in his home named Raven.
Grown up, Erik is on a hunt for vengeance against Schmidt, traveling the world to find him. Xavier graduates from Oxford, Raven still at his side, after finishing a thesis over mutation. Meanwhile, a CIA agent MacTaggert discovers a plot by Schmidt, now known as Sebastian Shaw, to incite World War III. Moira goes to Xavier for advice on mutation and the CIA agrees to sponsor he and Raven at a secret facility.
Xavier finds Shaw as Erik is trying to kill him. Shaw escapes and Xavier takes Erik to the secret facility. They set out to recruit other mutants to join their team. While the pair is gone on a mission, the facility is attacked by Shaw. As Shaw carries out his nefarious plans elsewhere, Xavier moves the base of operations to his family manor.
Shaw convinces the USSR to set up missiles in Cuba and the newly trained team of Xavier's X-Men go to stop them. Erik locates Shaw and kills him, against Xavier's wishes, to avenge his mother's death. Both the U.S. and the USSR turn their missiles on the mutants. Erik stops the attack but Xavier must stop him from turning the missiles back on the fleets. In the fight, a bullet fired by MacTaggert and deflected by Erik hits Xavier and paralyzes him. Erik forces the team to take sides and leaves, now as Xavier and the X-men's enemy.