Ship has suffered an anomaly and must run a check while X-Factor gets back to their lives. Each member does their own thing, but an all-out assault on Ship brings everyone back to the fray. The Dark Riders attack X-Factor while Harddrive attacks Ship. Apocalypse is seeking revenge, and this is just the first step.
Note: This issue includes the Apocalypse Manifesto, an in-depth look at members of X-Factor through the eyes of Apocalypse himself. This issue includes files on Archangel, Cyclops, and Jean Grey.
X-Factor prepares to practice in their Ship's version of the Danger Room. Before the sequence can start, however, an odd power short occurs, leaving Cyclops concerned over the well-being of Ship. Ship claims it wasn't more than a hiccup but promises to run a diagnostics check anyway. With the power back on, Ship unleashes an intense practice sequence. Iceman is a bit upset about the intensity, but Cyclops urges his team to do their best.
Unknown to X-Factor, that little glitch was caused by one of the Dark Riders of Apocalypse, Harddrive. Hardrive taps in to Ship's systems and the Dark Riders watch the practice session. Apocalypse drills his Riders on how to attack each member of X-Factor and the Dark Riders give satisfactory answers. Once each member of X-Factor has been discussed, Harddrive announces that he can no longer hold the link because of Ship's defenses. Apocalypse allows Harddrive to sever the connection. He explains that attacking X-Factor is good, but the real objective is attacking Ship, because nothing should ever cross Apocalypse.
With the practice session over, and Cycolps unimpressed by the team's effort, Archangel and Iceman head out on the town. Archangel takes flight and reminisces about what Apocalypse did to his wings. Just then, a helicopter flies past and Warren acknowledges that the wings recoiled on their own. He continues his flight and ends up at the home of Charlotte Jones. He knows he shouldn't be there, but he's spotted before he can decide to leave. They have a frank discussion about losses in their lives and embrace one another. At Ship, Cyclops and Jean discuss Xavier's Dream and how they need to be their best in order to fight for it. They also end up kissing. Iceman meets up with Opal and entices her to take lunch. The two enjoy an ice-ride around the city. The Beast, on the other hand, watches his lady, Trish Tilby, on TV as she reports from the Gulf. Her topic is on countries using mutants as weapons, but nobody seems to want to start that yet. Beast sighs and hopes it never has to come to that.
Cloaked from detection, the Dark Riders crash their small craft into the side of Ship. Cyclops and Beast search Ship and finally find the breach. Cyclops mentions to Beast that the two are alone, as Archangel and Iceman are out on the town and Jean is in the nursery. Having overheard, the Dark Riders thank Cyclops for the information and proceed to attack. With just two members of X-Factor to deal with, Tusk, Gauntlet, and Barrage get the upper hand.
Meanwhile, Psynapse finds Jean and immediately begins toying with her by taking her to the Astral Plane, a place that Jean no longer has any abilities in since her telepathy abilities have been lost. Psynapse manipulates Jean's mind into making her think she is a girl again. Digging too deep, Psynapse triggers Jean's psi-link with her team and each member can hear her. Cyclops and Beast fight all the harder and Archangel and Iceman also join the fray once hearing Jean. Tusk and Barrage are taken out while Jean is still being tortured by Psynapse. The Dark Rider wants to dig a little deeper; he has questions and probes further into her mind. He triggers something that sends him in a fit, releasing Jean. Jean then comes to the rescue of her teammates by instinctively using telepathy to shut Gauntlet down. She doesn't know how she does it, but any sort of investigation is cut short when X-Factor notices that the small craft the Dark Riders crashed into Ship has started sprouting some kind of virus.
Elsewhere, Apocalypse smiles, knowing his plan for Ship is going as planned.