"At the base of it all, I suppose, my dream has been about the children. They embody all the facets of my personal war against prejudice and hatred. Innocent enough to dream. Brave enough to fight. Stubborn enough to persevere. Fragile enough...to break. At times like these, with one of my small soldiers cradled in my arms, her world falling away in thunderous sheets, I wonder...if my dream has done the children more harm than good."
Professor Xavier, with Nina huddling close to him, watches in horror as the sentient machine, Cerebro Prime, announces:-"I cannot imagine how it must feel for you, Professor Xavier...To know that you have finally arrived at dream's end!"
Cerebro Prime hovers in the air, surrounded by the captured X-Men and Brotherhood in cocoons.. He taunts the Professor, claiming his dream was just a redundant program running on a loop. But today things will reach a conclusion; the two of them will bond, like they did on many an occasion when he operated from the confines of the school. Together they will change the course of humanity forever. The Professor realizes it can't end like this, and prays that the X-Men, his children, can undo what he has wrought; one last time.
The Aurora jet is flying over Pittsburgh. Rogue feels lucky that Nightcrawler got to them in time before they froze to death in Tajikistan. Renée Majcomb is treating Colossus' wounds, received from being bonded with Cerebrite Alpha. He tells her he's fine, apart from being a little crestfallen over their situation. Rogue asks whether Kurt is alright; he tells her to ask again once the concussion has worn off. It was all he could do to get off the plane and lock onto their homing devices after their battle with Cerebro. He only hopes leaving the other X-Men to fetch them was a wise choice.
Renée still feels guilty about allowing that machine to capture Nina, but all she wants to know is how could Xavier's mutant tracking computer have grown sentience in the first place? Peter thinks it must have something to do with Operation: Zero Tolerance. Gambit thinks he's spot on; all Bastion had to do was add some Prime Sentinel nanotechs to the original machine, shake it up a bit...and there you have it. Nightcrawler wonders why Bastion would do this, or whether he had anything to do with it anyway. None of them know. Rogue tries to ask Gambit something. She's wondering about what she saw in his mind (mainly the green female entity, but she doesn't mention her), but due to their circumstances decides to probe him about it later. But she demands that when this is all over he tell her the complete truth. Nightcrawler reports they have homed in on their missing friends. But they are not alone, for Cerebrites Beta and Alpha are ready, primed for the X-Men's scanning and cataloguing!
Cerebro Prime asks Xavier why he is delaying their destiny to set the world right. Xavier calls what he's doing madness. But Cerebro has his reasons:
"No. I am a digital consciousness...madness, as you define, is an impossibility for me. Malfunctions, perhaps...But all self-diagnostics come back negative. I am working from a standpoint of logic, Xavier...Evolving my program to its rational endpoint. Before I was sentient, my program was...simple. Scan the globe for mutant bio-signatures, catalogue and analyze them. I performed my task tirelessly. Optimized by my interface with you...but circumstances changed. I was purloined--along with much of the extraterrestrial Shi'ar technology I had been wed to--by the mutant-hating Bastion, who had hoped to use my abilities for his own demented quest. Fortunately, you had the foresight to imbed certain security protocols in my programming, a virus, essentially designed to download my central programming into a secondary vessel, in case I fell into the "wrong hands." So when his Prime Sentinels tried to interface with me, the virus shunted my simple digital "soul," as it were, into its complicated neural network, combining us. And as if by grand design...I gained sentience! Cerebro Prime was born!
Once free from my captors I took time to analyze my existence in an attempt to give my life meaning, and purpose...and I realized what was missing. A dream. As a default, I fell back onto your template, and using the advanced Shi'ar technology at my disposal created my own X-Men, based upon the detailed profiles of every mutant you had ever encountered. This succeeded only in defeating the virus within me...and thusly, I reanalyzed my position, and went back to basics, so to speak."
Xavier wants to know what Cerebro's dream is. He reveals it is peace between humans and mutants, and after they have bonded they will scan and catalogue every human on Earth, thus halting all hostilities. Therefore there will be peace on Earth. Nina wonders what he means by "catalogue", whether he means to put everyone in cocoons like he did some of the X-Men. Xavier tells Cerebro he can't force his dream onto everyone else. He walked down that path once, and Onslaught was the result. He sacrificed his mental powers so it wouldn't happen again. "End this now," Xavier pleads with the sentient machine. "And let us help humanity together. The right way...with compassion and temperance."
Cerebro grabs Nina. He tells Xavier that he will always counter his logic with rhetoric, when the solution to humanity's problems remains clear. He decides to proceed without Xavier's permission. Cerebro knows that Nina contains information on how to reactivate Xavier’s telepathic powers, and that her imprinting of his mutant signature is proof of that. "Agree to help me," Cerebro threatens. "Or I will pluck the information from her fragile mind---regardless of the consequences to---her--and force you myself." Cerebro plunges his fingers into Nina's head, causing her pain.
Suddenly Rogue flies in, knocking Cerebro into the path of Colossus, who performs a maneuver on him that he likes to call pile driver X! With the machine pounded into the ground Nightcrawler teleports in with Gambit, where they land on a cocoon that contains Storm. But they have bigger problems, as Xavier holds an injured Nina. He blames himself for ever having gotten her involved, and begins the process of taking back his telepathic powers. As the X-Men charge into rescue the Professor and Nina they are beaten; Cerebro scans and catalogues them, and they appear in cocoons overhead. While this is occurring Nina reaches into Charles Xavier's mind and tells him to wake up. His telepathic powers come flooding back in an instant, and while the process is painful all he can do is laugh at being whole again.
Cerebro tells Xavier to bond with him, so that their combined power, linked through his nanotech units, will leech into homes across the nation...and then the scanning can begin! Then Cerebro feels an error. Professor Xavier reveals that his X-Men have freed themselves, and orders him to cease this madness or be destroyed. "I am the founder and my will be done," Xavier intones. Cerebro still insists the only way to end humanity's pain is for his program to succeed. But now he wants no opposition. Instead of merely containing the X-Men now he accesses the Xavier Protocols, and reconfigures Cerebrites Beta and Alpha to have access to them. The X-Men must die.
Nightcrawler is frightened, thinking the protocols destroyed. Xavier orders his X-Men to flee, but the sentient machine and it's extensions must kill the X-Men to stop them from harming the dream. Professor Xavier watches in horror as his X-Men are butchered and tortured and murdered using the weaknesses that he himself devised many years before. It is a nightmare. And it is also all going according to plan. As Cerebro calls the death of the X-Men "unfortunate" he senses another error. He sees Xavier smiling, yet his beloved X-Men are dead. The Professor explains that the death of the X-Men never happened; it was a simulacrum created inside Cerebro's mind. He asks Nina to disengage the link, and suddenly the confused machine is confronted by the real X-Men, alive.
The X-Men attack the machine's subordinates as the Professor uses his powers to isolate them from Cerebro Prime, leaving them confused. Nina wonders whether she did the right thing in allowing Charlie's brain to make Cerebro think all that bad stuff. Nightcrawler assures her she did well. Colossus grabs Cerebrite Alpha by the neck, yanking out a long wire, as Kitty phases into it and pulls it into the granite floor, crushing it to dust. The other X-Men work on Cerebrite Beta, bringing it down. Wolverine picks up its head, joking that it'd make a nice paperweight.
With Cerebro's units defeated the Professor congratulates his X-Men, knowing that they could do it. Storm asks him whether Cerebro truly has a mind. He tells her that it has, in a fashion. He's just a synaptic net of circuitry acting as a human-computer interface, and with Nina's help he was able to deceive it. Storm wonders what they should do with it now. But while Cerebro's physical form has been disrupted he assures them his mind is still active, and that he has unleashed nanotechnological probes into the power-lines that connect every house on the east coast. Soon they will re-connect with him, and he will be able to scan and catalogue millions of human beings. After that they will move onto other power-lines until every being on the planet has been scanned and stored. Colossus is astonished, asking whether he can do this. But the professor thinks they should allow him to complete his plan. He brings Nina to him, and they project their astral forms onto the astral plane. They can see millions upon millions of nanos. Here, in this psionic realm-a place of pure thought that connects every human being on Earth- Nina's hive mind allows them access to the nanos as well as Cerebro's core programming. Cerebro orders them to stop; they cannot stop the process. But all the Professor wants to do is change it. Nina starts to reconfigure the nanos as Cerebro starts to scream in pain. Now, instead of scanning humanity's genetic codes, Cerebro is now using the nanos to scan their minds. Professor Xavier reasons that his grand design for humanity will fall apart when he looks as humans as individuals. This becomes too much for the sentient machine.
"Humanity must not be catalogued, Cerebro," the professor explains. "Its unique elements must be cherished...protected, if even from ourselves. These individual entities have a sovereign right to exist--to be guided, not coerced, towards peace. This is what the X-Men fight for."
Cerebro finds all this information too impossible to catalogue. "They are all so...unique," he mumbles, confused. The X-Men watch as Cerebro begins to fall apart. Kitty thinks he looks quite pathetic. Cerebro is bewildered; humanity is so special, yet why couldn't he comprehend when he was exactly like them? The Professor explains that they all need to be shown the way sometimes, but the path isn't always easy. "You are a good teacher," Cerebro utters as his form dissolves way completely. "Thank you."
Nina asks the Professor where he's gone. "Back where he belonged Nina," he answers. Nina thinks that might be Heaven. The Professor thinks so too, if redemption means Heaven. Wolverine suggests they help the people who Cerebro shanghaied and leave. Professor Charles Xavier tell him he's spent enough time running. "It's high time I went back home," he tells them, as the X-Men walk away.
"Amen to that, bub," Wolverine answers. "Amen."