It is now eight years since Rachel Summers transported Scott “Slym”, and Jean “Redd”, into the future. Nathan Dayspring continues to hone his telepathic powers under the tutelage of his mother, but wonders why his parents insist he hide his cybernetic arm. After discovering that his parents are involved in a secret rebellion, Nathan must determine if he should side with his family, or Apocalypse.

Jean finds herself going through her old lessons with Nathan in an attempt to help him control his mutant powers. By night, however, Jean and Cyclops accompany the Clan Rebellion on missions attempting to overthrow Apocalypse. This mission, the group finds the progenitor to the Legacy Virus, are attacked by Ch'Vayre, and find a first meeting between Cable and Stryfe. The Clan also witnesses the mutant powers of the Dayspring family.

Synopsis

In the "comforts" of Coastcrest, Jean walks Nathan through her old lessons in controlling telekinesis. Nathan, after much effort, is able to mask his techno-organic body parts on his own. Tired, Nathan nestles into Jean's arms as she thinks on his future.

In Citadel Apocalypse, Stryfe shows off his growing psionic powers by murdering a human. Apocalypse dismisses Stryfe and Ch'Vayre comments that he is concerned that Stryfe is missing out on his childhood. Apocalypse makes very clear that he cares nothing for Stryfe's childhood, as he firmly believes Stryfe to be Nathan Summers, whom Apocalypse infected with the techno-organic virus yet the boy seems to have fought off the disease. He will use Stryfe to become the new vessel of Apocalypse's soul.

Later that night, Jean and Cyclops meet up with Prior Turrin to assist in another covert mission against Apocalypse. They don't realize that Nathan has found them out and stows away on the mission.

The rebels infiltrate a research laboratory and find files regarding the creation of the Legacy Virus. Ch'Vayre and Stryfe attack with some troops and push the rebels further into the laboratory. Cyclops and Jean decide to finally allow their powers to be seen as they fight back, which surprises both the rebels and Ch'Vayre's troops.

Meanwhile, Nathan hears the voice of Rachel/Mother Askani in his head and she walks him through setting up a self-destruct program in the laboratory computers. Stryfe finds Nathan and the two realize that they not only look alike but that they seem to share thoughts. Stryfe tries to rid the world of Nathan, a clearly lesser being, but Rachel helps Nathan open his mind to the full use of his present powers and the energy knocks Stryfe unconscious. This burst of power also throws Nathan's body into flux.

The fight below comes to an end when Prior Turrin orders an evacuation once bombs are charged. The rebels flee (with Nathan, after he lets them know he is present) and the laboratory explodes. Nathan then tells Jean about the voice in his head named Rachel.

Later, Cyclops visits a discreet room in which lays Rachel. Cyclops apologies to the comatose body for never giving her a fair chance, but thanks her for helping Nathan.

Elsewhere, Ch'Vayre comes to the realization that he can no longer stand idly by as Apocalypse turns Stryfe into a murderous vessel.