Ship has exploded, but managed to save its core systems and construct a survival module around the X-Factor team.
X-Factor joins with the Inhumans to get Blue Bolt's people back, as well as get Cyclops's son back. Apocalypse, however, has amassed a large enough army to make these tasks difficult. But he won't destroy X-Factor... at least not yet. It's an attack on the moon base of Apocalypse.
X-Factor is somehow alive in a cocoon supplied by Ship. Ship communicates to Jean's mind that another ship is approaching and pulling them in. Fortunately, it's Black Bolt and a team of his Inhumans. They alert X-Factor that Apocalypse has taken over their home on the Moon, as well as many of the Inhumans themselves; the Dark Riders being a select few. Medusa, in fact, has also been taken captive. As Jean relates to the attack by Psynapse, Crystal runs from the room. Karnak explains that Apocalypse is good at pitting family against itself, as Psynapse is Crystal's cousin.
As a side note, the tale of the mysterious woman is told. She is Askani and belongs to a future world run by Apocalypse. Her mission is to be sent back in time to protect Nathan Christopher from some evil. Time travel is difficult, however, and her body, transported as pure energy, does not reincorporate as hoped. She is merely a being of energy taking on her former form by her sheer will. Her mission is to protect the son of Cyclops, but so far she's done a terrible job.
On the Moon, X-Factor and Black Bolt's squad talk about their situations. Beast explains how Ship and he worked out a way to download core elements of Ship's personality into a survival module that helped protect the group from being killed. Cyclops and Black Bolt "talk" about the next move. It seems Apocalypse has taken the Inhumans and their city as his base on the Moon and Black Bolt is afraid of a full-on assault because of how close the Watcher's home is. Just then, Foxbat and Gauntlet appear and kidnap Crystal from right in front of X-Factor's eyes. Cyclops is done with skirting around Apocalypse. The bad guy wants a fight, he's going to get one.
Apocalypse muses in his chambers about Nathan Christopher. Simply put, to ensure the future of Apocalypse the boy must die. The intention is to absorb the boy's life essence into that of Apocalypse. Just then, Apocalypse is told that an army of Inhumans is outside and ready to attack the stronghold. Outside, Ship states that he is performing a ruse. The army amassed is simply an image created by Ship to draw out the forces of Apocalypse. Once the army arrives at a specific point, Karnak and Gorgon unleash an attack that opens a chasm under the army. Iceman buries them. As the ruse fades, Cyclops leads a real team against the prison and frees a majority of the Inhumans. Having got the Inhumans back, Black Bolt leads them against the Riders of the Storm, those Inhumans that actually switched sides. X-Factor heads through the Citadel. It's almost too easy. The finally break into the chambers of Apocalypse. Cyclops tries to blast him when a voice explains that they aren't the only ones who can pull a ruse. A huge Apocalypse is seen towering over everyone that announces that the time has come for X-Factor to die. Just below, Nathan Christopher is contained in an odd contraption.
Sebastian Shaw has just received the worst news of his life: his company, the one he's built from the ground up, has just been bought by some unknown person. That person reveals himself to be Shinobi Shaw, Sebastian's own son. Why would he do this? Shinobi notices that his latent mutant powers have finally started kicking in and they resemble more those of Leyland's than his own father's. Shinobi has the ability to phase in and out of things. He reaches in to his father's chest and manipulates his heart. He then blows up the estate. Shinobi is then seen crawling through the wreckage.