Plot
In the far future, human X-Man Tom Skylark evades a pack of Crawlers (foot soldiers genetically engineered from Kurt Wagner's DNA, along with those of Madrox, Scott Summers, and others) amongst the ruins of the X-Mansion. His Sentinel partner, Rover, dispatches the Crawlers. Tom is met by E.V.A., a representative of the Xavier Institute, now an interspecies organization. Together, they transport the Phoenix Egg, found on the Moon, to the X-Men's secure headquarters in the Manhattan Crater. But a Crawler has hitched a ride inside the compound, replicating itself with Multiple Man DNA and attacks. E.V.A. and Tom are rescued by a bird-man named Tito (descended from Beak), but the Phoenix Egg is teleported back to the Crawlers' master and creator: The Beast, a white-haired Henry McCoy.
The "Three-in-One" Stepford Cuckoos relate the downfall of human civilization throughout history to Wolverine, to which Cassandra Nova adds recent bad omens. She says that something in the past went wrong to give the Earth such a dystopic future, but no one knows what exactly. One hundred-fifty years in the past, at the grave site of Jean Grey, Cyclops gives up on superheroics and changing humanity, turning down Emma Frost's offer to re-open the Xavier Institute as well as her offer to begin a real relationship with her.
Back in the future, Tom Skylark relates how the Proud People of the Starlit City, the last free outpost in Europe, fell to Apollyon the Destroyer, herald of the Beast. Their sacrifice allowed him to escape with the Phoenix Egg, but Tom laments his losing it. E.V.A asks him to join the X-Men for one last direct assault against the Beast. The Cuckoos speak before Wolverine and Cassandra Nova of the consequences of defeat: genetic enslavement by the Beast, loss of all natural evolution and species propagation. When asked to look hard and unblinking at the future, the Cuckoos see judgment by the Phoenix. As Beast hatches Jean Grey, a living fire-goddess, from the Phoenix Egg, she recognizes him as Henry, but he says he is much older than that, that now his name is Sublime.
The Phoenix annihilates the Terminds, an insect species in Panafrika, but an encounter with X-Men liaison Bumbleboy spurs old memories in Jean's mind, calling Beast's plans of destruction into question. At the edges of Beast's Transatlantis territory, the X-Men engage the Crawler army, but despite a minor victory, Wolverine sees Jean Grey amidst the reinforcements, clad in a revealing black variant of her Dark Phoenix outfit. Cassandra, working in the X-Jet with No-Girl, instructs her to remove the Phoenix Crown, which gives Jean back her memories and returns her to a human form. Logan shows Jean the truth of Beast's history: John Sublime was a host for the Sublime bacteria, a sentient lifeform billions of years old that infected countless species and sowed aggression and conflict to ensure its genetic dominance, so that no one species would ever be hardy enough to outlast it. U-Men, super-Sentinels, nano-viruses, etc. all created by an underlying disease. When Scott Summers left the institute, Hank McCoy tried to manage things, but things fell apart, and when he tried the drug Kick to cope with the stress, he was infected by Sublime (the true nature of the "drug").
Cassandra, pleased with her work, exchanges one more conversation with Martha before the Beast, possessed by Sublime and with the power of the Phoenix, kills her. The other X-Men all perish at the hands of the Beast, who declares himself supreme, ready to 'Remake God in [his] Image!' - only for Jean to reveal that they were not an attack force, just a distraction. Smiling, she removes Sublime from Beast's body, briefly returning him to normal. Seconds after apologizing, he is decapitated by Apollyon, who promptly unmasks and finds the world not as perfect as hoped. In an extra-dimensional plane within the ancient M'Kraan Crystal called the White Hot Room, numerous other hosts of the Phoenix (most notably Quentin Quire) instruct Jean, now dressed in a white and gold version of her Phoenix costume (thus establishing her as the White Phoenix of the Crown), to repair the broken timeline. Reaching back in time, Jean pushes Scott "to live". Cyclops agrees to re-open the institute, and stand side by side with Emma Frost for the future.
