Up in the air in Sinister’s ship, Beast sends out some S.O.S. signals. No one is responding, and he and Forge wonder if the whole world could be assimilated already. Forge confirms Beast’s hypothesis that the rate of conductivity is the rate of assimilation, and that mutant tissue can’t be assimilated yet. Sinister says that it might be the reason why his lab was attacked: it was the largest database on mutant genetics. Together with the information out of Cerebro, the Phalanx might be learning how to assimilate mutants. Forge urges their need for a lab, and Beast comes up with Muir Island. It might still be unassimilated cause of it’s isolation.

In the Spire, Hodge introduces himself to Wolverine as affiliated to the Genoshan government. Hodge says that the mutants there cost him an arm and a leg, but thanks to the Phalanx he’s got them back. In return he became their guide on Earth. Hodge explains to Wolverine that through his metal skeleton the Phalanx will explore mutant genes from the inside.

On Muir Island Moira says it’s possible that they are the only ones left unassimilated. Amelia Voght brings Beast some coffee. Beast is surprised to see her there working as a medic. Outside, a seagull lands on Sinister’s plane, and his beak touches it. It immediately is assimilated by the Phalanx. Back inside, Banshee has joined the crowd. Forge managed to develop a virus that attacks both the computer part and the organic part of the Phalanx. Warlock wants to know what happens to his life-mate after the virus invades the Phalanx, and Forge admits they’re not really sure. Beast suggests more research, but Warlock says, no. If his life-mate must die, he will die with her, acting as a bait to infect the virus. Warlock alarms when he senses the Phalanx nearby. They all run outside to Sinister’s plane, but it transforms into a Phalanx unit right before their eyes. Banshee and Sinister start attacking the unit, but it has little effect. Moira drags Amelia inside to try and save the patients. Sinister asks why Forge is not using the virus. Forge starts blasting at the unit with a gun; saying that they do not have very much of the virus, and that he doesn’t know what it takes to destroy the core.

They hastely retreat inside, and encounter Moira. Forge asks her where her plane is, but she wants to save her patients? Forge stresses that the world might be lost if they don’t act soon. Moira seems convinced and takes all of them to the plane. The Phalanx is on their heels, and Banshee fights the unit as the others board the plane. His sonic scream does seem to affect the unit, but the entire floor is made out of metal, and tentacles soon capture Banshee. The plane is already taking off, but Moira stands to close to the door shouting to Banshee, and is captured by tentacles, too. Beast tries to hold on to her, but Sinister thinks it’s too dangerous and pushes her out. Moira is assimilated, and as the plane takes off they see how Muir Island is entirely assimilated. Amelia tells Sinister to set course to Antarctica, because she knows a friend who can help.

As the covenant stand in front of a citadel, Forge says there’s no entrance. Sinister is about to blast away, but Amelia holds him off. She uses her mutant power to transform them all into gas and takes everyone to the other side. They enter the main room in the base, and discover Magneto! Magneto asks them what they want? Amelia explains the situation. Magneto is not pleased they broke in and brought a vile creature like Sinister into his sanctum to asks him for help. Sinister is about to start a fight, but Beast holds him off. Beast stresses the fact that Magneto’s own life is in danger. Magneto doesn’t seem to care, and explains he is weary of life since Asteroid M was destroyed. However, Beast convinces Magnus when he says Quicksilver is among the captured mutants, and that they cannot save him without Magneto’s powers.

Magneto, entirely covered by Warlock’s matter, takes off to St. Johns in Newfoundland to collect a sample from a small Phalanx tower. They are soon discovered, and escape in a magnetic force field to the plane. They take the sample back to Magneto’s estate. The captured sample transforms into a head of Hodge. Warlock alarms that Hodge was the one who captured his life-mate. After Genosha, Hodge joined the U.F.O. research with the government, and the Phalanx found him. He had explained the importance of assimilating mutants to the Phalanx, and so they made him a guide to Earth. Hodge says that the Phalanx mean to assimilate all organic life in the entire universe, that it is more efficient to reproduce in a digital way, and eliminat genetic differences.

When they’ve heard enough of Hodge’s nonsense, they integrate the virus into the force field, and the matter transforms into what it was before; brick stone. Thus, there is hope for the assimilated humans; they might have a chance at returning back to normal. They take off to the Spire, the Empire State Building, in New York! Meanwhile in the Spire, the Phalanx manage to assimilate Gambit. Hodge thanks Wolverine sarcastically. The core starts to assimilate the remaining mutants one at a time, beginning with Xavier. Xavier expresses his anger towards Hodge.

Moira’s plane flies above New York, and the insiders are plotting the assault on the Spire. Forge says they’ll begin below the central chamber, where all the other captured mutants are. Amelia takes herself, Forge and Mr. Sinister inside, and Forge turns a device on creating a force field. He instructs the others to find Jean and Lorna before the force field wears out. Amelia frees Jean from her cell, and Forge frees Polaris. Next, they begin collecting offensive power. Sinister ironically frees Cyclops, and Cyclops starts attacking Sinister, but Amelia explains Sinister is on their side. They all enter the force field, backed up by Jean and Polaris.

Magneto, Beast and Warlock enter the core with the virus in a magnetic force field. The core identifies them, and Hodge starts making fun of Magneto’s beard. He uses tentacles from the Nexus to try and break Magneto’s force field. Magneto fakes that it collapses, and Warlock is captured by the Phalanx. According to plan, Warlock infects the core with the virus, which begins transforming back into it’s original matter. The Empire State Building and everything else are returning to normal, including all the humans and Cameron Hodge.

Magneto and Beast check on Warlock to see if he’s all right. Warlock is all right, but they fear his life-mate is gone. However, Warlock picks up her electronic pattern again, and flies towards the signal. He restores her from some pieces of techno-organic matter. Thankfully, he can’t remember any of the horror of her past few weeks.

They all meet up in front of the Empire State Building, and Xavier expresses his happiness of the weird cooperation that came out of the threat of the Phalanx. Magneto says that the Earth is practically still the same. Cyclops wants to go after Sinister, but Jean tells him to let it go. Warlock asks help from Forge and Beast to get back to his home planet to free it from the Nexus forever. Quicksilver walks in on the scene and he and Magneto hug.