Ship has been infected with some type of virus that makes it lash out at the city, as well as X-Factor themselves. But this isn't all Apocalypse has planned. Baby Christopher is also a target and is soon a captive of the Dark Riders despite X-Factor's best efforts, as well as the efforts of a mysterious woman who calls herself the protector of the "Chosen One."
Note: Originally Scott and Jean were to be married in this issue, but that was changed. The original cover was later published in an issue of Marvel Vision.
Also, this issue includes the Apocalypse Manifesto, an in-depth look at members of X-Factor through the eyes of Apocalypse himself. Featured are files on Iceman and Beast.
Errors: On the very first page, Ship is called "sentitent." It should be "sentient." Also, on page 15, a speech bubble is given to Harddrive, though it is Beast that speaks.
New York is being destroyed by offshoots of Ship. Archangel saves a bum from being impaled while other heroes (like Captain America and She-Hulk) combat in their neighborhoods. Inside Ship, X-Factor is unable to ascertain how Ship is being infected. Jean, however, is somehow able to make a fleeting contact with Ship with her consciousness. She learns that the infection seems to be killing Ship. Harddrive, still tapped into the X-Factor base, uses a tentacle to attack Jean, effectively taking her out of the picture. The tentacles then attack the rest of the team. They find the attacks to be weak. With Jean unconscious, Cyclops finds it odd to hear a voice in his head. It tells him that his son is in danger. The team heads to the nursery.
In the nursery, Foxbat has found Nathan Christopher and plans to abduct him. From seemingly nowhere, a mysterious woman springs to attack the Dark Rider, calling herself the boy's sworn protector. She knocks out Foxbat and then looks at the child. She mentions something about arriving from another time and knowing that Apocalypse must behind this attack. Just then, a group arrives and she attacks. Archangel tries to pin her to the wall with his feather-spikes but she seems unaffected; they pass right through her. She then realizes that she's attacked the family of the boy. She also realizes that this little sidetrack was enough for Foxbat to awaken and steal the son of Cyclops. In agony that she wasn't able to fulfill her mission, the mysterious woman vaporizes part of Ship's wall and escapes to rectify her mistakes. Harddrive then uses Ship to attack X-Factor. The tentacles aren't too strong. Beast comes up with a plan.
Outside, Sergeant Charlotte Jones and other members of the New York Police Department prepare to enter Ship to find some way of shutting down the destruction. After a statement of defense for her mutant friends, Jones enters Ship alone and is surprised that none of her colleagues found entrance beside her. Her walkie-talkie doesn't work so she uses a private line Archangel had given her. Upon making contact with Beast, Jones is attacked. In the meantime, Beast has hooked himself up to the central net of Ship in hopes of personally finding some way around the infection. Ship, seeing that its systems are terminal, uses what power it has to blast into space. Back to Jones, she's being held by Gauntlet when Archangel blasts through and frees her. Barrage states that the Dark Riders are through messing with X-Factor for now and they are teleported out of Ship.
Beast hooks back up to Ship when the tentacles come back to attack. Cyclops gives a stirring speech about how Ship can't give up, but Ship explains that there is nothing it can do. It must self-destruct. Also, Ship lacks the power to preserve the lives of X-Factor after the blast. Beast frantically tries to find a way to preserve some semblance of Ship, as well as the team, before the self-destruct occurs. He finds something.
Ship explodes in space. On Earth, the mysterious woman watches in sorrow. She vows that she'll do whatever it takes to regain the Chosen One, little baby Nathan Christopher.