The storyline featured many controversial elements, such as Cyclops moving forward with his relationship with Emma Frost (prompted by his dead wife), the Stepford Cuckoos being revealed as a development in the Weapon Plus Program, John Sublime being a sentient bacterium bent on bringing evolution to a halt and hints that the Xavier Institute student Ernst and Cassandra Nova are the same person.

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.

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.

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.

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.