The sentient spacecraft Ship is attacking the citizens of New York. A homeless man is about to be infected with one of Ship’s techno-organic tendrils when Archangel swoops down to his rescue. In another part of the city, Captain America and Sersi battle to protect innocent citizens from the random attacks. The Thing and Human Torch blast through the tentacles and ponder the fate of X-Factor’s team members, while She-Hulk has one of her court cases interrupted by Ship’s assault.
Aboard Ship, Beast examines the vessel Apocalypse’s strike team breached Ship’s hull with. His most sophisticated probes cannot penetrate the vessel’s shields. Iceman and Cyclops notice Marvel Girl acting oddly and are concerned after Psynapse’s attack. Jean tells them she hears a voice in her head and realizes it is Ship, who is sick and dying.
Harddrive, who is monitoring them from inside the vessel, lashes out at the team with Ship’s tentacles and manages to stun Jean. Suddenly, Scott hears Ship’s voice, quietly warning him that Nathan Christopher is in danger. Beast scoops up an unconscious Marvel Girl and the team takes off to the nursery.
In the nursery, Foxbat holds a sleeping Nathan inside his enclosed carry-cot. As he turns to leave with the toddler, a woman appears through a portal, claiming to be “Lord Nathan’s” chosen and sworn protector. She quickly takes down Foxbat with an energy dagger and grabs hold of Nathan.
She is thankful to have arrived in time, and vows that Apocalypse shall never claim “The Chosen” as a child or a grown man. As she gazes upon Nathan, wishing she had time to tell him the many things he needs to know as these are the last moments of his childhood and the end of his innocence, she quickly turns and fires at the approaching X-Factor. She curses her error for not sending Nathan away the moment she arrived, as she wrongly thinks X-Factor are Foxbat’s teammates.
Iceman is taken down by her attack and Archangel fires his neural-disruptive wing blades to incapacitate her. As she is hit, she realizes who she has attacked-“the Chosen’s” family! Archangel’s spikes do not work on her, but it gives Foxbat an opportunity to snatch Nathan and teleport away. The mysterious woman bemoans that she may have sacrificed her life for nothing as she burns a hole through Ship’s hull in pursuit, leaving X-Factor to wonder if she is an enemy or ally.
Harddrive notes that Ship’s systems are 73% corrupted and has the walls launch a brutal attack on X-Factor, although the tendrils aren’t very strong and Archangel can slice through them and Iceman freezes them so they shatter. Beast notes that they are only fighting the symptoms, and need to treat Ship’s disease.
Outside, a group of New York’s police force, headed by Sergeant Charlotte Jones, prepares to enter Ship. One of the men jokes why Jones isn’t wearing her special superhero uniform. As they try to enter, only Charlotte get through the barrier and tries talking to Ship, but gets no response. She then contacts X-Factor on a special frequency through her walkie-talkie, but is cut short by Gauntlet, who strikes her.
Meanwhile, Beast does a hard-wire link with Ship and can finally communicate with the spacecraft. Ship informs Hank that Jean was right - he is dying. He then tells the team that he will not serve his former master willingly or be enslaved again. The massive spacecraft then begins disconnecting itself from the earth’s surface and blasts off into the sky, where he will engage the self-destruct sequence and destroy himself.
Charlotte Jones is squirming in the clutches of Gauntlet, who is debating her worth as a hostage. The floor suddenly explodes beneath them and Archangel flies out to rescue his girlfriend. Before he can engage Gauntlet, Barrage tells him and Tusk that Apocalypse has recalled them and they teleport away.
Charlotte and Warren join the others, with Cyclops trying to convince Ship that suicide is not the answer. Ship disagrees, saying it’s the only way and hopes the team can forgive him, as he does not have the resources to help them escape and survive the explosion. Cyclops berates Ship, telling him that suicide will only give Apocalypse the victory he wants, that life and freedom only mean something if you are willing to fight for them. He also reminds Ship that the enemy has his son and destroying X-Factor would rid Apocalypse of the only beings to defeat him. Ship replies that he can no longer maintain the safety of the compartment the team is in and it’s too late to stop the self-destruct.
The walls start lashing out at them, and are no longer susceptible to Bobby’s ice. The tendrils quickly overtake him, but Charlotte takes them out with the weapon she took from Gauntlet. Beast remains linked to Ship and is frantically trying to reroute the systems to regain control. As the tentacles close in on them all, Beast initializes Ship’s systems, but it seems to be too late. Ship explodes into pieces, high above New York.
The mysterious woman looks upon the explosion and cries out. Could her interference have caused the death of the family of “The Chosen”, she wonders. She has no way of knowing, but vows to save Nathan from the clutches of Apocalypse, no matter the cost.