High above the Earth, the shattered remnants of the sentient Ship are scattered across space. Inside its central core, Ship telepathically contacts Jean, as it senses a spacecraft nearby. The spacecraft locks its tractor beam on to the survival module and pulls X-Factor aboard.
Inside the craft, they are greeted by a members of the Inhumans’ Royal Family: Karnak, Blackbolt, Gorgon, Crystal and her dog, Lockjaw. They face a common enemy, as Apocalypse has seized the Inhumans’ Great Refuge on the Moon and turned some of their people into his “Riders of the Storm”.
Jean says that they’ve already met some of the Riders, who were the strike team that attacked Ship and X-Factor. She tells them they kidnapped Cyclops’ son and that Pynapse psychically attacked her. Cyclops asks Jean how she knows what the names of their attackers were, as they are unaware Jean’s telepathy has re-emerged, but is interrupted by Crystal running from the room. She was also attacked by Psynapse, a close cousin, and is worried about the fate of her sister, Medusa.
The mysterious protector of the Chosen named Askani prepares for her return to the past to save young Nathan from Apocalypse. Her comrade, Boak, tells her they have a lock on the Chosen but know nothing of his current predicament. Askani starts to discorporate, turning to pure energy. She arrives in the present, but is unable to return to corporeal form and has to will herself into the shape of the woman she was and sets off to find Nathan.
Up on the moon, Hank explains to Bobby that core elements of Ship’s personality were transferred into the survival module it formed around X-Factor after the blast. Gorgon shows Cyclops the stronghold Apocalypse has built. Scott inquires about launching an assault, but Blackbolt has insisted on being circumspective in their approach due to their close proximity to the home of the Watcher.
Suddenly, a flash bathes the room in red light, indicating the teleportation arrival of the Riders of the Storm. Foxbat grabs hold of Crystal, while Gauntlet strikes out at Iceman. Foxbat warns Gauntlet not to harm Iceman too much, as Apocalypse wants to kill X-Factor himself. The Riders then teleport away with Crystal as a hostage, attempting to lure X-Factor and the Inhumans into a direct attack.
In Apocalypse’s command center, his scientists inform him that Nathan is resisting them. Apocalypse tells them this is understandable, as Nathan knows Apocalypse is his enemy. Apocalypse intends to absorb Nathan’s life essence into his own, killing the infant and eliminating him as a future threat. One of Apocalypse’s minions rushes in, telling him a large force has gathered outside the fortress, preparing to attack.
Outside, Charlotte Jones is astride Lockjaw, somewhat in disbelief that she is fighting up on the moon, yet excited as well. Ship shares in her excitement and apprehension, as he has projected holograms of some members of X-Factor and the Inhumans in front of the fortress to distract Apocalypse’s forces and hopes they do not see through the deception.
The Riders of the Storm and five different Apocalypses confront them. Beast hammers down on the moon’s surface with all his might, as Gorgon stomps down at the same instant. Karnak the Shatterer joins in, hitting pressure points that reveal a crevasse beneath Apocalypse’s oncoming force. As the enemy plummets into the fissure, Iceman covers them in a blanket of ice and revels in their success. Marvel Girl warns him not to be so cocky, as they know how dangerous Apocalypse can be.
While Ship’s holograms of them fight out front, the real Cyclops leads Archangel, Blackbolt and other Inhumans in blasting through the slave pens. Charlotte can’t believe the power of Blackbolt, whose mere whisper carries the kinetic impact of a bomb. The team quickly breaks through and X-Factor leaves the Inhumans to deal with the army and the Riders of the Storm while they go after Apocalypse himself.
As the members of X-Factor battle their way towards Apocalypse, they become uneasy. They have entered the Blue Area of the moon, where the energy being who replaced Jean Grey, known as Phoenix, committed suicide. Jean has Phoenix’s memories and relives them like they are her own-this is where she died! Warren’s wings react with his memories of this place, and he wonders if Apocalypse had anything to do with the destruction of Dark Phoenix and wants a shot at the real Jean.
X-Factor quickly defeats the mechanical copies of Apocalypse, but realize they are getting through too easily. However, to get to Nathan they must walk into the trap that has been laid for them and Cyclops uses his optic blasts to blow out the door. Inside, Apocalypse congratulates Scott on deducing it was a trap. Scott unleashes another powerful optic blast, but discovers it is only a hologram of his enemy. An enormous Apocalypse is revealed, with Nathan techno-organically attached to him. Apocalypse taunts that X-Factor has had its fun-now it’s time for them to die!
In a chalet outside of Interlaken, Switzerland, Sebastian Shaw discovers he has been bought out and has lost control of all his companies. He is stunned to discover that it is his own son, Shinobi, who has ruined him. Sebastian lashes out at his son in rage, striking him and telling him he had to work from the ground up to build his empire, which also fronts his world-wide covert mutant operations. Sebastian would rather see Shinobi dead than lose all he’s worked for and starts to strangle his son.
Shinobi turns the tables when he uses his newfound mutant powers of controlling molecular density to reach into Sebastian’s chest and give him a heart attack, while making a snide suggestion that perhaps Sebastian’s friend Harry Leland was his real father. The chalet then explodes into a fiery ball, but using his powers Shinobi appears to be the only one who survives the blast, having set off the bomb himself to murder his father and his associates.