Scott Summers and Hank McCoy are preparing for a team evaluation sequence aboard the sentient Ship, X-Factor’s headquarters, when Ship malfunctions and the lights go out. As Scott reaches for an emergency power pack, everything goes back online and Ship ensures Scott and Hank that it was just a hiccough and starts a diagnostic review.
Scott informs the rest of X-Factor, that with the X-Men gone, it is up to them to look after things and they have to be at their best. At his command, Ship launches an intense battle simulation, reminiscent of the X-Men’s Danger Room.
Unbeknownst to the X-Factor team, they are being watched. Apocalypse and his henchmen analyze the team during their training exercise, noting their strengths and weaknesses. Foxbat will handle Cyclops; Gauntlet will tackle the Beast; Tusk will focus on Archangel; Psynapse will attack Marvel Girl; and Iceman is left for Barrage.
Hard-drive, who has been hacking into Ship’s defenses for them to watch X-Factor, cries out that Ship is reacting to her intruder program and is trying to cast her out. Apocalypse tells her to sever the link and praises her good work for allowing them to spy on the team. He then warns his henchmen not to underestimate X-Factor and reminds them that their true target is Ship, who dared to betray him.
Back aboard Ship, X-Factor has finished the evaluation sequence and Scott is not impressed with the team’s performance. He informs them that he is disappointed in their lack of teamwork. Bobby reminds him that it’s just an exercise and they always come through in battle. Scott agrees that X-Factor is good, but if they had been better maybe some deaths could have been avoided.
Later, Archangel flies high above the city, pondering his transformation into the horseman Death and breaking free of Apocalypse’s control. Lost in his thoughts, Warren barely misses colliding with a helicopter and is saved by his wings, which reacted instinctively to avoid the collision. Warren swoops down into the heart of Brooklyn and meets with Charlotte Jones, unsure if she wants to see him again.
Charlotte tells him she saw the news from Genosha and it sounded awful. Warren tells her that that is what his life is like, both as Warren Worthington and Archangel. She reminds him that it is no different for her, that danger finds you whether you are a cop like her or a superhero. Warren worries she might get hurt, but Charlotte tells him he’s worth the risk as they embrace.
On board Ship, Jean tells Scott that he was hard on the team. He replies that he doesn’t want any more deaths among them and the enemies they fight are getting stronger and better and they can’t afford to make more mistakes. In the old days they had less dangerous foes. Jean reminds him that their lives have never been easy, from fighting Magneto to the Sentinels, but that making the world a place where mutants and humans are accepted as one is worth the price and the good they do does makes a difference.
Bobby greets Opal at the record store where she works and invites her out for lunch. She tells her co-worker, Rick, that they’ll be back in an hour. Bobby jokes, unless they are attacked by aliens and kidnapped to the other side of the cosmos. As Bobby ices up and takes Opal soaring up over the buildings on his ice slide, she warily asks him if he’s just kidding. He reminds her that things like that happen to X-Factor all the time but he’ll always be there to rescue her.
Meanwhile, Hank watches television and sends a memo to Scott that the preliminary results from Ship’s diagnostic show no abnormalities. Trish Tilby is reporting from Saudi Arabia covering the first Gulf War and Hank worries about his love being in the middle of a war and hopes she’ll be careful.
Later, Hank and Scott discuss their concerns over Ship’s system problems. Suddenly, Apocalypse’s strike team slams into Ship with their cloaked vessel, breaching Ship’s hull. Cyclops and Beats quickly try to locate the breach and are attacked by Barrage, Tusk and Gauntlet.
Elsewhere, Marvel Girl encounters Psynapse and he assaults her on the Astral Plane where her telekinesis is useless. Psynapse taunts her and mentally reduces her to a child, where she relives the death of her best friend Annie and her first telepathic awakening.
Suddenly, all of X-Factor’s members are psi-linked through Jean and Iceman and Archangel are alerted to the fight and rush home to Ship to join the battle.
Archangel takes out Tusk, who falls onto Barrage, allowing Iceman to encase them both in ice.
Meanwhile, Psynapse holds Jean’s head in his hands on the Astral Plane, preparing to tear into her private thoughts when Jean manages to strike back telepathically and disables him. She then joins the others and telekinetically shuts down Gauntlet, now his name and his capabilities thanks to the newfound telepathy she isn’t quite aware of yet.
X-Factor’s celebration at defeating the intruders is short-lived as the vessel that breached Ship’s hull releases techno-organic material that starts burrowing into Ship. Cyclops asks Ship for its status but receives no reply. On board the vessel, Hard-drive informs Apocalypse that the infection of Ship’s primary cybernetic core has begun, and with all its defensive systems inoperative, Ship’s prognosis is terminal!