This story arc continues from X-Men #83 - The Hunt for Xavier! Part Four: Tomb of Ice.
Within his Florida facility, Cerebro Prime proceeds with his plans to 'catalog' all mutants, and, most significantly, capture Professor Charles Xavier. However, he receives a notification that his base has been detected by human air surveillance, so Cerebro uploads all his data to his mobile unit, and then initiates a destruct sequence. He also discorporates his surrogate X-Men, stored in stasis tubes, minutes before the facility explodes behind his escape jet.
Within the prison on Alcatraz Island, the X-Men (Wolverine, Nightcrawler, Shadowcat and Marrow) and the Brotherhood of Evil Mutants (the Blob, the Toad, the Mimic and Post) unite to protect Professor X from Cerebro's proxy unit, designated Cerebrite Beta. Wolverine severs its arm, but it pins him under its foot. As it regenerates its hand, Shadowcat tries to tend to Xavier who was partly caught in the collapse of the wall through which Cerebrite Beta burst, but Post, claiming some right to the Professor, warns her to leave him to the Brotherhood's care.
As the battle proceeds, Cerebrite Beta 'catalogs' the Toad, who disappears, apparently disintegrated. Nightcrawler allows Mimic to borrow his teleportation ability and together they shift the construct to a lower level. Nightcrawler makes it back, and with the Cerebrite gone, Shadowcat phases herself, Xavier and Marrow through the floor in an attempt to escape the renewed attention of Blob and Post.
Cerebrite Beta then collapses the floor from below, and all the mutants, save Nightcrawler, fall into the gaping hole. He teleports to the X-Men's jet, which is cloaked and parked in Golden Gate Park, and tries to contact the other X-Men, unaware that they, too, are currently in combat against Cerebrite Alpha, another of Cerebro's agents.
As Cerebrite Beta re-engages the other mutants, Shadowcat tries to lead Xavier and Marrow out of the prison, but inadvertently re-enters the battlezone. Marrow confronts the construct to provide a distraction and Shadowcat and Xavier make good their opportunity to escape again. The Cerebrite follows, with the mutants chasing after it, but it finds Shadowcat and Professor X. As Wolverine catches up, he witnesses the Cerebrite 'catalog' her, and, thinking her dead, he goes berserk, decapitating his opponent.
Mimic explains to the X-Men that the entity is an agent of Cerebro, which had been Xavier's mutant locating computer until Bastion's meddling resulted in the system's gaining self-awareness. He then attempts to fly away with the Professor, but the Cerebrite, having reconstructed itself, 'catalogs' Mimic. Wolverine rushes to his fallen mentor, who tells his students he still feels Shadowcat's mind, meaning she's not dead, but rather, has been somehow moved to Cerebro. He concludes the best way to get to her is to allow themselves to be 'cataloged' as well.
At that moment, Nightcrawler, piloting the jet, arrives above the prison in time to witness Xavier, Wolverine and Marrow vanish in a flash of light emanating from Cerebrite Beta. With no other option, he sets a course for Tajikinistan in hopes of finding the rest of the X-Men.
This story arc concludes in X-Men #84 - The Hunt for Xavier: The Conclusion! Dream's End