Magneto feels that the human race is ready for extinction, ready for replacement by Homo Superior, and plots against them with his Brotherhood of Mutants. The pair is brought to Professor Xavier. Rogue is offered a place to learn to use her power surrounded by other youngsters with similar problems. Wolverine is offered help in finding out about his past. Though ever distrustful, Wolverine decides to throw in his lot with the X-Men for the time being.
Rogue begins to find a home within the school.
Momentary peace is disrupted by the plans of Magneto. A genius at physics, he's constructed a machine that can harness his own powers to mutate the genes of human beings, making them mutants. After demonstrating the machine on Senator Kelly, he plans to turn it on a United Nations gathering near Ellis Island. Magneto's Brotherhood has hints of being more disjointed and widespread, but only a few agents are used. Other characters from the series show up in the background, or in cameos, but don't interfere if they have no purpose in the story.