In its Florida base Cerebro Prime demands an update from his computer. It tells him this:
"Summation of current activities regarding mutant search and subsequent disclosure. Methods: Bio-signature trace for failsafe identification. Mission parameters in geographic terms: worldwide. Duration: unspecified. Island of Manhattan: of 9.57 million scanned. Bio-signature recognition of twenty-three latent mutants. Subjects cross-referenced: verification certain. M.C's program excludes Morlock tunnels beneath city. System subset adjustment. Alert: Subject designate Magneto: self styled master of magnetism. Subject's movements allotted highest priority. Monitoring resources sufficient currently. Continual whereabouts : update available as per voice recognition. See systems mode: RS7-3 Alpha/P update."
Cerebro Prime orders the computer to keep tracking Magneto; they'll come for him when they have collected the X-Men. The computer warns of air surveillance over the facility, and threat of human penetration. Cerebro Prime has all his files downloaded for transference to their mobile base, and shuts the systems down and orders complete erasure of the entire facility. The countdown begins as Cerebro Prime flees, recapitulating his prior decisions: taking on the guise of Professor Xavier and creating holographic surrogate X-Men. The plan turned out tobe ineffectual. The surrogates, currently held in stasis tubes, are terminated, having become expendable and are bombarded with anti-protons.
His mission has to go on; to seek and obtain and catalogue mutants for re-education. As Cerebro Prime escapes in a fighter jet, and the download of files is complete, the facility explodes, and he heads to a power station on the East Coast, where he states:-"Facilitation of man/mutant cooperation continuing."
Alcatraz Island, San Francisco:
Professor Xavier bemoans his lack of powers, his telepathy lost during the Onslaught crisis, as he recovers from the explosion caused by Cerebrite Beta. He can only watch as the Brotherhood of Mutants, who rescued him from the Hulkbuster base, and the X-Men, who tracked Xavier here, begin to battle it out with his former Cerebro unit, which has somehow gained sentience due to Bastion's tampering!
The battle isn't going well. Wolverine's bone claws do no damage. Marrow figures her bone growths wont do any either. Blob tries ripping out the thing's wires, getting in the way of Post who tries to fire concussive bursts at it. Mimic has used all his powers (the powers of the original five X-Men) and has gotten nowhere. Shadowcat wants to try phasing inside the thing to do damage from the inside. Nightcrawler warns her to be careful, thinking that, just as he, Kitty and Peter rejoin the X-Men due to Excalibur being disbanded they end up battling this reject from "Alien!" Add to that joining with their former enemies, the Brotherhood of Mutants.
The battle continues as Wolverine wonders what that thing is. Blob tells him that Xavier called it the end of mutant life as we know it. "Chuck's been wrong before," Logan throws back as he charges in. Cerebrite Beta scans him, cataloguing him, and prepares to collect him. A glow emanates from one of it's hands, but Wolverine hacks the hand off with his bone claws. The thing pins him down with it's leg, refusing to allow Wolverine to escape, as it re-grows its arm.
Kitty tells Marrow to stop fighting with Toad and help Wolverine as she goes to help Professor Xavier, highly emotional at finding him alive, only to see him injured in an explosion. She asks him what that thing is after him. He tells her it is called Cerebrite Beta, an extension of another entity known as...
"Release him and step away, or suffer the consequences," a voice tells her from behind. Kitty thinks it's Cerebro, but the person identifies itself as Post.
Nightcrawler tells Mimic that a machine that can heal itself might be impossible to beat. He suggests that Mimic copy his teleportation abilities so they can remove the threat below with no further injuries. As Marrow jumps on Cerebrite Beta, hacking at it with a bone growth, the thing catalogues Toad and collects him, shooting a blast that vaporizes him. Wolverine and Marrow watch in horror, thinking Toad to be dead. Right then Mimic and Nightcrawler teleport in, each grabbing a shoulder of Cerebrite Beta, then they teleport out with it again. Wolverine is free of its grip.
Blob tries to pull Professor Xavier away from Kitty, as does Post. Kitty asks them if Toad's death meant anything to them. Post counters with the threat that more of them will die if the Brotherhood does not escape with Xavier. Wolverine charges in, telling the Brotherhood that Charles is family. Marrow isn't convinced; she once again reminds the X-Men that Xavier did nothing for the Morlocks, her people, so she's a little less sympathetic.
Nightcrawler teleports back in, minus Mimic and Cerebrite Alpha, and looking in bad shape. Blob demands that the carnival freak tell them where Mimic is. "Was? Carnival freak? Have you forgotten, my fine fat friend, that Fred J. Dukes was discovered by the X-Men in just such a place?" Nightcrawler remarks, insulted. then explains that he and Mimic took the entity below...but it was ready for them, and he will be back.
Wolverine tells Blob to back off from Nightcrawler. Blob tells him they've no idea what they're up against. Post fires a blast at Wolverine, knocking him out of the way. He threatens to do the same to Kitty's head if she doesn't take her hands off the creator right now. Kitty is not sure where his misguided loyalty comes from towards the professor, but warns him that Xavier will only be leaving with the X-Men. Marrow yet again wonders why the X-Men are treating Xavier like they were the knights of the round table helping some kind of fallen King Arthur. The way she sees it it's all Xavier's fault for turning into Onslaught. Kitty grabs her hand and phases them both, and the Professor, through the ground into the basement, away from the Brotherhood. Blob orders his useless Brotherhood to get after her before she phases Xavier out of the prison completely.
Suddenly Cerebrite Beta bursts through the floor, still on a mission to catalogue and collect mutants. But the stress on the ground is too great; the floor collapses, taking Blob, Wolverine, Mimic and Cerebrite Beta down into the basement. Nightcrawler hooks his tail onto a pipe to keep from falling, thinking he will be of more use to the X-Men up here. So he teleports to the Aurora jet, still cloaked in Golden Gate Park. This move leaves him spent, his powers exhausted. He sends a mayday out to the other four X-Men in Russia, figuring that they haven't found the Professor as they found him here...
Colossus, Storm and Gambit are fighting another extension of Cerebro, named Cerebrite Alpha, and aren't having as much luck either. Rogue looks on with terror, the telepathic girl Nina in her arms, as her friends are beaten...
Golden Gate Park:
Nightcrawler isn't getting a response from the other X-Men. He wonders what they could have found, and deduces that no response from them is as clear as them shouting for help.
In an Alcatraz sub-basement Kitty and Marrow are trying to move an injured Xavier to safety. He trusts Kitty to get them out of the maze-like passages they find themselves in. "So far today..." Marrow sulks. "...I've been teleported, phased and attacked. What next? The sound of an explosion answers her question. Marrow guesses they're not safe yet, but at least she's used to wandering around tunnels.
Blob, Post, Mimic and Wolverine land in a boiler room. Post has weapons ready to go; Blob is unhurt. Mimic has broken a leg though, and is in pain. Wolverine answers that he's broken a few ribs, but his healing factor is taking care of them. Cerebrite Beta charges in, still determined to catalogue and collect them. Wolverine reveals that the only advantage they have is speed, so they'd better get out of the machine's line of fire. Mimic can't move though, but Blob orders Post to leave him behind. Wolverine wont though, and urges Mimic to use his wings to escape, which he does, just as a blast from Cerebrite Beta hits the exact spot where he had lain.
Kitty, Professor Xavier and Marrow are still lost in the basement tunnels. Xavier suggests phasing through a couple of walls, but she's not sure of the layout of the place, and it could be a risk. Still, she considers phasing blind to be the only option they have.
Cerebrite Beta corners Post and Blob, about to catalogue them, when Kitty, Xavier and Marrow unluckily phase into the room, where the sentient machine turns his sights onto it's primary target: Xavier himself. Marrow jumps on the machine, attacking it, giving time for Kitty to phase Xavier through more walls and get him to safety. Kitty tells the Professor that, for all her sarcasm and bitterness, Marrow may yet become a great X-Man. Wolverine grabs Marrow as Cerebrite Beta flings her off to pursue Xavier, and he suggests they go after him quickly. By now Blob has had enough, and wants to get away from the machine as quickly as he can. Wolverine tells him he can either help or be gutted by him at this very moment. They need all the help they can get taking down this machine.
Kitty is phasing Xavier through wall after wall. She remembers a time when the X-Men were at Alcatraz during the Beyonder affair. Now she figures she's moved them outside the complex into the exercise yard, and from there she can phase them both through the retaining wall around the yard. Just as she's about to phase Cerebrite Beta finds them and catalogues Kitty, but Mimic fires an optic eye beam at him, allowing Kitty and the Professor to phase. Only this route leads to the edge of the cliff, and she had to phase back through the wall again. She hopes it will be too busy fighting to notice them; but no amount of interference from the X-Men and Brotherhood stops it from collecting Kitty; vaporizing her instantly, like Toad. "Kitty!" Wolverine screams, grief stricken. He charges at Cerebrite Beta, hacking its head off with his bone claws. Marrow goes in for the kill with her bone grafts too, slashing at it.
Thinking the creature defeated Blob thanks them for their help, but he still wants Xavier to come with them. "We're still not safe," Mimic explains. "Remember, the defeat of Cerebro's pawn is still no defeat itself." Wolverine wants to know who Cerebro is. Mimic explains, as he flies off with the Professor in his arms, that the Cerebro was somehow given sentience by Bastion; intentionally or unintentionally, they don't know. A decapitated Cerebrite Prime is repairing itself with nanotechnology, and catalogues and "collects" Mimic in a beam of vaporizing light. Xavier drops to the ground. Wolverine asks him to pull it together so he can tell them how to stop Cerebro before it kills anymore of their friends. The Professor tells him that Cerebro didn't kill anyone; he just sent them somewhere else. Marrow figures that they have to save Kitty if she's alive; and Wolverine knows the only way to do that is to allow Cerebrite Beta to take them too.
At that moment Nightcrawler is flying over the prison in the Aurora jet. Suddenly he watches in horror as Logan, Marrow and Kitty are vaporized by a beam of light sent by Cerebrite Beta. He decides, if there's any hope left at all, to go to Tajikistan to find the other X-Men. "One way or another," he vows, as the jet speeds towards Russia. "I will find my team-mates...if they are yet alive!"