In Apocalypse’s citadel, the consciousness of En Sabah Nur is being prepared for its new host, Stryfe. Meanwhile, teenager Nathan Dayspring is dying from the techno-organic virus that has plagued him since birth. After struggling between life and death, Nathan finds a way to exist on the astral plane, and encounters his half-sister Rachel Summers.

Ch'Vayre turns on Apocalypse and attacks with Jean's help. Meanwhile, Nathan fights for his life as Cyclops looks on. Nathan pulls through and the Dayspring clan unites to stop Apocalypse from transferring his soul into Stryfe. Cyclops and Jean are then sent back into their present with Jean taking the name of Phoenix.

Synopsis

Ch'Vayre begs Apocalypse to abandon the designs to accelerate Stryfe's maturation so as to be the next bodily host for Apocalypse's soul. Apocalypse has grown tired of Ch'Vayre's second-guessing and expels him from the citadel.

In Coastcrest, Nathan's puberty is sending his techno-organic parts into flux, which puts Nathan into a coma. Turrin is not optimistic the boy will survive, but Jean believes she can guide Nathan subconsciously to getting better. Inside Nathan's mind, however, he meets up with Rachel - at least an imprint of her. Rachel explains that Nathan is far stronger than he knows and will have to use his incredible telekinetic powers to stave off the techno-organic virus at a cellular level to stay alive. Nathan fights and takes control over his body just as those outside are ready to declare him dead.

During Nathan's inner struggles, Turrin and Jean have left Cyclops in order to complete a three-year operation to prevent the Legacy Virus's creation. The two are ambushed by Ch'Vayre, however, and Turrin is left immobilized. Ch'Vayre offers to help Jean stop Apocalypse, who is in the middle of transferring his essence into the body of Stryfe. Jean and Ch'Vayre interrupt but are blasted away. Nathan senses that Jean is in trouble and urges Cyclops to help.

Apocalypse turns back to Stryfe and attempts to enter the boy's body but is rejected. Apocalypse is stunned, as he realizes that Stryfe is not a true mutant, but a clone. He tries to enter the body anyway but finds that Stryfe resists. This resistance is aided by Cyclops, Jean, Nathan, and Ch'Vayre. They attack in unison and Nathan disrupted the psionic link between Apocalypse and Stryfe. Apocalypse divines the identities of his attackers as Professor Xavier's old students, but this is short-lived as he is quickly dispatched due to his frail frame.

With the battle won, Jean realizes that she is no longer in the body of Redd Dayspring but on the Astral Plane with Rachel. Rachel asks Jean to take the name of Phoenix back to the present. Meanwhile, Cyclops says his last goodbye as he is pulled out of the body of Slym Dayspring. Cyclops and Jean are sent back to the present.

Ch'Vayre explains that he has enough resources to hide himself and Stryfe but that Nathan will have to be on his own. Nathan determines that he will stop at nothing to take down the world Apocalypse has created.