[Note: This story arc continues from The Uncanny X-Men #364 - The Hunt For Xavier! Part Five: Escape From Alcatraz]
Within a former power plant on the east coast, Professor Charles Xavier huddles with his fellow captive, Nina the Mannite, below Cerebro who boasts of his achievements as he hovers amidst the nanotech pods which contain a multitude of mutants. According to Cerebro's programming, it has taken Xavier's dream to its logical extent, saving mutantkind by cataloging and storing them.
Meanwhile, the X-Men's Aurora jet speeds over Pennsylvania, heading toward the signal the aircraft's tracking indicates is the location of their captured teammates. Aboard are Nightcrawler, who is piloting, Rogue, Gambit aod Nina's guardian, Dr. Renee Majcomb. They near Cerebro's base, where they are met by two of his Cerebrite agents.
Below, Cerebro explains his origins to Xavier: originally, it had been a relatively simple computer with which the Professor cataloged and analyzed mutant bio-signatures across the world. Later, it had been augmented with advanced Shi'ar technology. When Bastion and his Operation: Zero Tolerance had taken over Xavier's mansion and school, he tried to purloin the system, but a security protocol installed by thé Professor had moved its programming and data to a secondary vessel. When Bastion tried to interface Cerebro with one of his Sentinels, Cerebro had gained self-awareness and escaped.
Cerebro had also developed a purpose: to take Xavier's dream of peaceful coexistence between mutants and normal humans to its logical conclusion by cataloging and storing all humanity, mutant and non-powered alike, bringing about a peaceful world.
To bring his plan to fruition, Cerebro tells Xavier they will bond once Cerebro learns how to reinstate the Professor's psychic powers. Xavier protests with an emotional appeal, at which Cerebro plucks up Nina, threatening to injuriously extract that information from her mind. Suddenly, Colossus and Rogue crash in through the ceiling to attack Cerebro. Nightcrawler teleports in with Gambit and they find Storm and other mutants and normal humans alive but cocooned.
Xavier has Nina mindlink with him to restore his psionic abilities, while the X-Men deal with Cerebro. However, Cerebro swiftly 'catalogs' the four mutants, encasing them in cocoons. Professor X experiences an inward flood of thoughts and emotions from the whole of humanity once his telepathic senses return, and he frees his X-Men from their pods. In response, Cerebro alters his tack from 'cataloging' to elimination, so he accesses the Xavier Protocols, a series of tactics to be used as a last resort should his protégés irrevocably turn against their mentor. Cerebro generates a number of agents, each tailored to a specific X-Man and based on the protocols.
Xavier watches in horror as his students fall to Cerebro, but then a smile slowly crosses his face. Victorious, but puzzled, the construct asks his maker why he seems pleased, so Xavier reveals that he and Nina created the illusion of the X-Men's defeat within Cerebro's 'mind'. The X-Men then press their advantage with a hammering assault, dismembering the construct.
As Cerebro rebuilds himself, he informs the X-Men he is currently dispatching his nanotech probes to all humans, still intent on analyzing and cataloging every individual. However, rather than opposing him, Xavier allows him to do so, and then he and Nina send their astral forms into the 'psychescape' to guide Cerebro. Xavier trains Cerebro's focus, not on each person's genetic code, but into each one's mind. After experiencing an overwhelming number of thoughts, hopes, dreams and emotions, Cerebro is finally able to comprehend the uniqueness of each member of humanity, successfully countering the logic of his previous programming.
Cerebro thanks the Professor for this 'lesson' and dissipates. Once he is gone the pods release the individuals stored within. As the X-Men turn to aid the former captives, Professor X tells his students it's time for him to return home.