A group of Mutants have stolen a shuttle, intending to find Asteroid M, and are being pursued by some S.H.I.E.L.D. agents. One the three pursuing S.H.I.E.L.D. shuttles is destroyed by a weapon fired from the Mutant’s shuttle. The leader of the S.H.I.E.L.D. agents, Harry Delgado, requests permission from the command station on Earth to return fire. A sudden electromagnetic spike and a flash of light brings the pursuit to an end.
Magneto arrives, floating in a force field bubble in space, and tears the ships apart. Magneto expresses his lack of interest in Earth’s status, citing environmental damage and violence amongst Humans, but will not allow these people to bring violence to his home. One of the Mutants that sought Magneto out begs him not to leave them to die. Magneto replies that he will merely return them to Earth with a warning that he does not wish to be disturbed again.
The female Mutant assures Magneto that he is the man her group came to find, with the intention of joining his cause. Magneto suggests that those days are behind him. The woman says that Magneto’s people need him now more than ever. She asks if he’s able to turn his back on his fellow Mutants or deny his destiny.
On Earth, at the Star City Cosmodrome in Baikonur, the Director-General of the Cosmodrome is informed of the destruction of the American shuttles in space and the cause of their destruction. He asks if there has been confirmation of Magneto as the cause. His colleagues confirm that it was Magneto and that he’s maintaining Asteroid M’s orbit 250 kilometres above them. They also report that his power levels have increased. The Director-General gives the order to inform Moscow and Washington that he’s initiating Stage One of the Magneto Protocols.
In Washington, at the White House, President Bush is briefing Colonel Nick Fury about the message from the Cosmodrome. The President understands their reaction and suggests that he’d probably do the same. He wonders if the runaway Mutants might be able to sway Magneto to their cause. Fury worries that if Russia acts rashly against Magneto it might make matters worse. The President asks what Fury would advise.
At Xavier's School for Gifted Youngsters, forty miles North of New York City, the X-Men are testing the building's defenses. They split into two teams, with the objective being to breach the defenses, locate and then capture Professor X. In one of the rooms of the mansion, Charles talks to Jean Grey about his return to the team and how he needs to learn the X-Men’s individual abilities and how they work as a team.
Charles wonders if he should have never left since his dream that Humans and Mutants could coexist peacefully seems further away than ever. As Jean glances at a photo of the New Mutants Charles wonders if he’d have been able to prevent the deaths of some of his students. Ultimately Charles questions whether his dream still has any validity. Jean assures him that it does or the X-Men would not still be a team.
Outside the mansion, the team of Rogue, Iceman, Colossus and Archangel are attempting to breach the defenses installed by Forge. Missile launchers prove to be a problem until Rogue, pursued by the missiles, flies back towards the launchers causing the missiles to destroy them. With that taken care of, Archangel launches Colossus at the mansion. Piotr changes to his steel form and smashes through a window into a room, where he is telepathically attacked by Jean.
Banshee informs Cyclops that the other team of Wolverine, Psylocke and Gambit are making their way past defenses under the mansion. Cyclops sends robots to attack this team to thwart their efforts in finding Xavier. Whilst Wolverine and Psylocke take care of the robots, Gambit splits off from them and finds his way to Jean’s location. He throws a playing card charged with kinetic energy at the wall behind Jean, kisses her and finds it was a trap as the robotic Jean and Professor X explode. This takes Gambit out of the contest.
The two different crews fight on board the Asteroid until Magneto stops them. One of them, Fabian Cortez, has a suggestion for Magneto. Back at the mansion the X-Men Blue team respond to a signal that Magneto is up to something. He has raised a nuclear submarine.
The X-Men confront him, but after a brief battle he flies off with the nuclear weapons. Rogue tries to follow him to talk, but is shot down by a Russian plane. Magneto is hurt and is healed by Cortez. Rogue is found in Genosha but is pursued by the newly formed Acolytes wanting her to join them. She disagrees and fights them, and the X-Men arrive to help her. Magneto turns up and declares that Asteroid M will be a haven for all mutantkind.
