In a Russian command center, scientists have discovered that the energy that destroyed the two remaining shuttles in space was indeed Magneto's power signature. There is discussion of activating the Magneto Protocols.

In the X-Mansion, the X-Men are in a Danger Room training exercise when Nick Fury contacts them with the information that Magneto has resurfaced. Rogue thinks that Magneto has changed and there is some discussion on what his motives truly are. The Professor, nevertheless, thinks that they should be prepared for anything. He then tells Cyclops that he agrees that the team should be divided into two to allow for greater flexibility in addressing threats.

Meanwhile, the military agents and the fugitive mutants begin to brawl inside Asteroid M. Magneto is unable to stop them as one of the agents shoots the mutant named Annemarie. Even near death, she professes her loyalty to Magneto's cause. Seeing one of his kind attacked in such a manner, Magneto takes control of the attacker's suit and kills him. The mutant Fabian Cortez, tells Magneto that the flatscans will not take this lightly and retaliate. He advises Magneto that certain actions must be taken to ensure his safety.

Later, Cerebro detects that Magneto has returned to Earth. Professor X then sends the Blue Team to confront him.

Magneto arrives somewhere in Russia where he previously sunk the Russian submarine, Leningrad. He discovers that the sub's nuclear missiles are still intact and he proceeds to acquire them to fortify Asteroid M's defenses.

Wolverine, Psylocke and Rogue then show up to stop Magneto, with the Blackbird nearby. Rogue tries to appeal to Magneto asking him what it is he is trying to do. Magneto claims that every act, including the sinking of the Leningrad, was done in self-defense. He then stops the Blackbird in mid-air stating that it is hovering too close for comfort. The rest of the team then drop in, and fighting ensues. Magneto reluctantly defends himself and is surprised at the ferocity of the blue team's attack.

Magneto, however, proves to be too much for the team and he begins to fly off with the nuclear missiles by his side. Rogue flies off to try to reason with him again, but is shot down by a Russian jet fighter. Magneto encases Rogue in a magnetic bubble and sends her to safety before he fires one of the nuclear missiles on the squadron of Russian jets.

In Asteroid M, Fabian Cortez uses his powers to heal Magneto's wounds.

In the Blackbird, Cyclops desperately tries to locate Rogue after the explosion. Professor X informs him that Rogue landed in Genosha.

As Rogue wakes up in a Genoshan hospital, Chief Magistrate Anderson informs her that they need her help since Genosha is under attack. Magneto' followers, now calling themselves the Acolytes, are attacking Genosha in search of Rogue and to punish the nation for its transgressions against mutants. The X-Men arrive facing off against the Acolytes until Magneto arrives.

Magneto reprimands the Acolytes for this unapproved strike. Magneto then declares that Asteroid M is now a haven for mutantkind. All mutants are welcome including the X-Men, and that should any harm befall any mutant, he will respond accordingly.

Review: This first issue of X-Men is top notch. It has the X-Men facing off against their first and most powerful enemy, what more could you want? The pacing of the story was perfect. Claremont made it a point to make sure that certain scenes did not drag on longer than they really needed to. My only problem in this issue would have to be the art. Jim Lee is one my favorite artists but it just seems that he wasn't up to par in this issue. I'm a little disappointed since he even took some time off of Uncanny to work on this issue. I was expecting something really great and mind-blowing but he fails to live up to my expectations.