Summary by Eben Rackland:
Magneto is back, and now that he is control of the Avalon space station the many nations of the world decide that something must be done to ensure the safety of humanity. Therefore, the Alpha and Beta options of the “Magneto Protocols” are enacted. This involves a defense shield, relayed between satellites, that disrupts the use of Magneto’s powers within earth’s atmosphere. Magnus, displeased by the defense shield, attacks the earth with a tremendous blast of magnetic power. When it strikes the earth, the blast is reduced into an extremely powerful pulse wave, which travels around the globe in a matter of mere minutes. The wave disrupts all electrical equipment, shutting off power in all corners of the world. It also crashes planes, and shuts down all types of medical equipment, and is basically responsible for hundreds upon hundreds of deaths.

Professor Xavier, perhaps blaming himself for his failure to stop Magneto in the past, assembles a strike team to go to Avalon, and fight the final battle with the master of magnetism. Xavier wears a Shi’ar exoskeleton that allows him to walk using psionic energy. He plans to lead the team himself, which is also made up of Wolverine, Gambit, Jean Grey, Quicksilver, and Rogue. When asked why the strike force isn’t larger and doesn’t include more original team members, Beast discovers that Xavier’s mission is more or less a suicide attack.

The team teleports itself to Avalon, using an override code for Avalon's systems. Colossus, the former X-Man, notices the security breach in the space station, but betrays his newfound Acolyte teammates by overriding Avalon’s internal security sensors. Xavier’s team is now free to move about the space station. By coincidence, they encounter Rusty and Skids, whom had opted to join Magneto. (X-Force #25) Having little time to spare, Xavier puts the two young mutants to sleep, much to the chagrin of a startled Jean Grey.

Quicksilver then takes a disk and speeds across the space station and loads it into a computer terminal, which gives the strike team control over Avalon’s computer systems. Xavier uses the computer to teleport Magneto’s Acolytes into the escape pods. He then jettisons the pods into Earth orbit, taking the Acolytes away from Avalon and any ensuing battle.

Magneto bursts in through a wall, taking away Xavier’s hope for a surprise attack. While their team moves to put an assault on Magnus, Jean and Xavier link their minds together in order to attack Magneto from within. Jean is reluctant to do this, because it goes against everything the Professor has taught her. As they strike Magnus in his mind, Quicksilver assails his father, confirming Xavier’s idea that this is the critical battle, where nothing can be held back. Magneto sets himself to murder his son Pietro, but before he can Wolverine leaps upon him, wounding him badly.

Jean breaks her psi-link with the Professor and tries to convince Xavier to end this altercation peacefully. That cannot be done, and Jean’s naïve ideas will cost her team immensely. Magneto, now in a fit of rage, magnetically grips Wolverine by his adamantium skeleton and lifts him in the air. To the horror of the X-Men, Magnus proceeds to rip the adamantium from within Logan’s body, nearly killing Wolverine that very instant. The only thing keeping his body together is the telekinesis of Jean Grey, only just commanding enough to keep Wolverine from falling apart.

Horrified and disgusted, Xavier finds that he has the courage to do what he’s never been able to do in the past. In despair over the probable loss of another of his beloved X-Men, he reaches into Magneto’s mind and simply erases it. Not possessing the mental power to hold his own limbs up, Magneto collapses.

Colossus comes, basically out of nowhere, and tells the team that Bishop is on his way in a Blackbird jet to pick them up and bring them home. He himself has chosen to stay aboard Avalon and take care of his leader, Magneto.