Anti-mutant hysteria is sweeping the nation after a small town in Missouri is set ablaze by a mutant. The news has driven William Metzger’s “Anti-Mutant Militia” into the spotlight and hundreds of youth are signing up for his cause to eradicate the mutant problem.
The FBI has caught wind of the uprising, and is worried about the civil unrest Metzger is stirring up within the country. Agent Duncan is sent to investigate on mutants. He is approached by Professor Xavier, who has snuck into Duncan’s office undetected. Xavier plans to convince Duncan, and the FBI not to come to a conclusion to start an annihilation of the mutant population.
In the dark of the night, a mutant vigilante, inspired by national heroes like the Avengers and the Fantastic Four, stops a thief from stealing a woman’s purse.
Professor Xavier is seen paying a visit to the Grey family. He is talking to the parents of Jean Grey into enrolling her into a “school” for mutants, to learn how to use her powers for self-defence.
Next, Professor Xavier applies for a job as a councillor at Freeport High School. He is there to monitor three other mutant teenagers enrolled at the school. Scott Summers and Bobby Drake, both recluses, and Hank McCoy, football superstar.
After watching the news reporting on Metzger’s recent slaughter of suspected mutant teenagers, Xavier sets Cerebro to work, scanning for mutants in need of protection and training.
Meanwhile, the FBI have been approached by Trask proposing to deal with mutants using “robotics”. Agent Duncan is forced to ponder the ethics of tackling the mutant situation: pulling strings to help out a mutant Charles Xavier strive towards peace or looking for means to eradicate mutants like his boss is inclined to do so.
The mysterious mutant vigilante is close to being identified as Warren Worthington, wealthy teen socialite and media darling. While on his nightly patrol routine, he is suddenly chased by a Sentinel. The Sentinel is taken down by Magneto, watching in a distance.