Jean Grey and Storm go out on a mission in the X-Jet, to find the mutant who attempted to assassinate the President. In an abandoned church they find Nightcrawler and discover that he may have been mind controlled.
Cyclops and Professor X go to see Magneto in his plastic prison, however they soon discover it’s a trap set up by Stryker. Magneto reveals that he was mind controlled by Stryker into revealing secrets about the X-Mansion and Cerebro, he and Charles are knocked out by gas while Cyclops is taken out by Lady Deathstrike. Cyclops and Charles are taken to Alkali Lake, while Stryker begins preparations to invade the school using Magneto’s information.
Wolverine returns to the mansion after trying to look into his past. Since all the other X-Men will be away, Professor X. asks Logan to look over the school, till they return.
Wolverine, Rogue, John and Bobby take Cyclops' Car and escape the mansion. Wolverine says they should find Jean and Storm, since Professor X. and Cyclops are currently unavailable. With the X-girls last known location in Boston, Wolverine decides to drive there. Bobby says his family also happens to live in Boston and that they should be able to take safe harbour with them. Stryker and his team take the stolen Cerebro parts to his base in Alkali Lake, so they can complete Dark Cerebro. The kidnaped students are also taken to Alkali Lake and thrown into cages for possible experimentation. Colossus leads the remaining X-Students who managed to flee the invasion to another safe house while they wait for the X-Men.
Mystique helps break Magneto out of his prison by seducing one of his guards off duty and injecting his blood with iron. Magneto is later able extract the metal from the guards body and use it to escape his plastic prison and meet up with Mystique.