Apocalypse does not forget too easily. Wanting revenge on X-Factor, he takes control of the Inhuman city of Attilan in the Blue Area of the Moon and subjects the inhabitants to imprisonment and brainwashing. Some of these new followers are made into the Dark Riders, or Riders of the Storm, and are sent to Earth to attack X-Factor, an assault that only proved to be a ruse, as the real intent was to distract the team while Ship was infected with some type of virus. With the first objective completed, the Dark Riders then kidnapped Cyclops's son, Nathan.
Having no other alternative, and to save the world from being destroyed, Ship propels itself and X-Factor into space and explodes (though preserving X-Factor and Ship in a nice cocoon of energy). X-Factor then meets with Black Bolt and the remaining Inhumans to take back Attilan and reclaim Nathan Summers.
The assault on Apocalypse's moon base is too easy, but that's only because Apocalypse wants to defeat X-Factor himself. The team confronts Apocalypse and has an epic battle, but the victory is overshadowed by the possible passing of Nathan and Ship. The mysterious Askani offers aid and Cyclops's decision will end up changing the Marvel Universe forever.
The child, Nathan Christopher Summers, is never seen again as an infant in the pages of X-Factor. His fate can be seen in the series The Adventures of Cyclops and Phoenix. The reader will then know for sure who he becomes. Also, a confrontation with Psynapse leads to Jean having some sort of telepathic powers, but nothing along the lines she'd experienced before.