High above russian space, a shuttle is pursued by three others. They manage to nail one of them and continue their desperate search for Asteroid M. Suddenly there is a blinding light and Magneto appears. With one gesture he tears all of the shuttles apart, refusing to allow their fight to endanger his space station. A female of the first shuttle tells Magneto that he can’t leave them to die, they are mutants who want to follow his cause. Magneto is amazed, he states that these days are over.
Scientists in a russian space center registered the magnetic activity in the atmosphere. The understand that it is Magneto, and that he must have rebuilt his base Asteroid M. They notify Washington and Moscow to initiate Stage One of the Magneto Protocols. In Washington the President and Colonel Nick Fury discuss the matter. Fury thinks that the Russians may make matters worse if they act without thinking. The president asks him if he has an alternative.
At Xavier’s school near Salem Center, Cyclops and Storm, the X-Men’s leaders plan to test the mansion’s new security systems, built by Forge.They have divided the X-Men into two teams, their task is to break into the house, then locate and capture Xavier. Jean acts as the professor’s last defense, and while they are waiting for the attacks, they talk about the past. Rogue, Iceman, Archangel and Colossus attack the front of the house. Missiles stop Iceman from making an ice slide, but Rogue presents herself as a better target and leads the missiles around till they crash into the missile-launchers. Meanwhile, Archangel has carried Colossusand throws him into the mansion, crashing through the window of the room where Xavier is hiding. However Jean stops Piotr telepathically, and Rogue gets knocked out by another wave of missiles. The first team has failed.
From the monitor room, Banshee notices the second assault team in the sewers below the mansion. Evidently Psylocke Wolverine and Gambit have slipped past the first arc of sensors, so Cyclops gives the command to have them intercepted by some robots. Whilst Wolverine and Psylocke fight them off, Gambit disappears. He manages to get to Jean and knocks her off her feet by throwing a charged card. Remy can’t help to take the chance and kiss her, as she explodes. Jean and Xavier were robotic duplicates, with the real ones being in the monitor room with Beast, banshee, Forge, Scott and Ororo. While they are still laughing about Gambit’s failure, a set of claws cut through from beneath the floor. Logan‘s senses were not fooled by the robot doubles, and with Psylocke telepathically masking his presence he got near enough the Professor. To proove that he has won, Logan pops the other hand’s claws right in front of Xavier’s head without hurting him. Cyclops gets angry, as he could have accidentally injured their mentor, and Logan leaves, even though Scott wants to run more Danger Room scenarios with the teams.
Later that day, Fury has contacted the X-Men and fills them in on the events in earth‘s orbit. Rogue defends Magneto’s actions, in fact the fight endangered his base, and so far they have seen no evidence of him having huirt or killed anyone involved. Cyclops disagrees, sharing the government’s concerns, but Storm reminds him that Magneto was their ally. Scott replies that before he was their enemy and leopards don’t change their spots. Wolverine’s opinion is that Magneto is just a man, and the X-Men to have been branded outlaws in the past. Xavier thinks they should be prepared for any eventuality and decides to follow Scott‘s suggestion to split the X-Men into two strike forces to allow for greater flexibility. He tells Fury that they will stay alert, and if more assistance is required, to get in touch.
The two crews from the shuttles awake to find themselves aboard Asteroid M. They continue their battle, and the mutants discover that their powers aren’t working. Magneto comes in, and orders his “guests“ to ceases their fighting. As Annemarie once more states that they want to join Magneto‘s cause, she gets shot by Deke, one of the agents, whose battle armour still functions.
Magneto gets angry and uses his magnetism to take control over Deke’s armour. He then makes him shoot himself. Major Harry Delgado apologizes for the incident, as Deke was acting without command; still he wants to take the apprehend the escaped mutants. Magneto says that whatever law office he is working for, it has no power in his home. He then tends to the injured Annemarie, and Fabian Cortez, another of the mutants introduces himself to Magneto. He wants to make the "flatscans“ (baseline humans) pay.
Soon afterwards, an alarm rings in Xavier‘s school. Cerebro has registered Magneto‘s signature over mid-Atlantic. Xavier tells Scott to depart immediatly with his Blue Team (Gambit, Beast, Wolverine, Psylocke, Rogue). They find Magneto raising the Leningrad submarine and extracting it’s nuclear missiles. Rogue, Logan and Betsy approach him. Rogue asks what Magneto is doing and he says that he will need the missiles for self defense. As he recognizes the rest of the team approaching in the Blackbird, he stops the plane in mid-flight, stating that he is not out for a fight, or otherwise he would crush the Blackbird. Beast and Gambit jump out, but Hank gets knocked out by magnetized wreckage and then Gambits finds his charged cards redirected back at him, knocking him out as well. Psylocke is able to kick off Magneto’s helmet, but before she can strike with her psi-blade, she gets pulled away by some cables. Wolverine attacks without hesitation and cuts Magneto, and when Cyclops realizes that his teammate has gone into a berserker rage, he blasts Magneto out of Logan’s range. He fimds himself inside the Leningrad, face to face with the remains of it’s crew. Seeing the skeletons he is reminded of his own past in a nazi concentration camp, and when Cyclops and Wolverine come after him again, he decided to simply take the missiles and leave.
Yet Rogue comes after him, she wants to talk instead of continuing the battle. She tells him that he has people spooked with his actions. Right as he starts to see her side of things, Rogue is shot down by a russian jet. Magneto is now convinced that peaceful coexistence is just a dream that will never come true. He returns Rogue to the ground in a magnetic bubble and then detonates one missile in russia‘s upper atmosphere before returning to his base.
On Asteroid M, Cortez recognizes that Magneto is bleeding. It’s a wound inflicted by Wolverine‘s claws. Magneto is shocked how ruthlessness the X-Men attacked him. He expected as much from Cyclops, but while he was with the team he and Logan fought side by side, yet the feral X-Men did not hold back. Cortez offers to heal him, like earlier did treat the wounds of his sister.
In the Blackbird, the X-Men are searching for Rogue, but neither their sensors nor Psylocke can pick up her location. Xavier contacts them from the mansion. Using Cerebro he can tell that Rogue is alive and fine, though he only learned of her location, when he received a phone call about her whereabouts from Genosha.
In Hammer Bay, Rogue wakes up in a hospital. Chief Magistrate Anderson asks her for help, as a cadre of super-powered terrorists are on a rampage through the city. Before she canmake a decision, the terrorists break into the hospital, they are none other than the mutants that wanted to join Magneto’s cause. They are after Rogue, and she is losing the battle when the X-Men arrive and help her. Gambit takes out Annemarie with a charged object, and Psylocke jumps on Chrome, using her telepathy to make him fly into a wall. Beast and Wolverine notice that one of them uses the name Delgado, like in Harry Delgado, the Major who had been pursuing them. Right as the Acolytes are defeated Magneto appears. He says that the Acolytes acted without his command and that the battle is now over. Yet he will not abandon the mutants who pledged themselves to his cause, and seeing how mutants are treated in countries like Genosha and all over earth, he will turn Asteroid M into a safe haven for mutantkind.
Meanwhile back at the mansion, Sean finds Moira in the lab. She is in tears and claims that everything that is happening is her fault.