The X-Factor goes after Apocalypse in "The Finale."
Cyclops must make the ultimate choice when he learns that both Ship and Nathan are shown to have contracted a terminal virus at the hands of Apocalypse. Askani offers a remedy, but there are no guarantees she's right about saving Cyclops's son. Apocalypse may be defeated, but his actions will haunt Cyclops forever.
Note: This issue isn't in the same format as the previous three issues in the arc. It is instead narrated by Cyclops.
In the chambers of Apocalypse, X-Factor comes face-to-face with the man himself. Apocalypse claims that the team will be obliterated by use of the very person they came to save: Nathan Christopher. At these words, Gauntlet, Barrage, and Tusk again attack. The fight is pretty quick with X-Factor making the fight look fairly easy, but then Medusa appears and distracts Cyclops. This is just enough time for Barrage to pump Cyclops in the stomach. Archangel attempts to attack Medusa but Crystal intervenes. The sisters seem to have momentarily switched sides.
A short time later, X-Factor finds themselves imprisoned and Apocalypse explains that he will have a new birth by incorporating their essences into his own. Just then, Cyclops's plan comes fully into effect. The Inhumans, who must have finished their fight outside, have stormed the chambers of Apocalypse. They free X-Factor and the groups attack the Dark Riders. Ultimately, Cyclops has the powers turned to Apocalypse. They sever the conduits attached to Apocalypse so as to stop any regenerative capabilities.
From the shadows, Askani watches and waits. Just then, Beast and Jean Grey approach Nathan's pod to release the boy. Askani, seeing their peril, jumps in front of Beast and uses her being of energy to dispel the field protecting Nathan. She introduces herself and instructs Beast to remove the boy before Apocalypse can do further harm. Apocalypse, free of his conduits, advances upon the combined teams.
Jean senses that something is wrong with Nathan. Ship confirms that the energy absorption process Apocalypse was using on Nathan has introduced a virus into the boy, summarily killing him. Beast asks if there is a way to reverse or retard the process and Askani states that she can save the boy, being her purpose for being present. Just then, Jean finds herself pulled into Nathan's mind by the boy's latent mutant powers. She states that such power could potentially enable Nathan to abate the effects the virus by sheer force of will, he just needs training. Apocalypse barges in and attacks Jean in Nathan's mind. He's sure of victory on both physical and mental fronts until Cyclops, being pulled in with Jean, severs Apocalypse with a psy-sword. In the physical realm, Cyclops has a difficult time coping with a mental battle. He decides to take out his mental anguish on the physical Apocalypse. He blasts the nemesis with everything he's got.
With Apocalypse out of the picture, Cyclops races to the side of Nathan. Sadly, defeating Apocalypse didn't reverse anything and Nathan appears to be worse off. Ship, with the little essence he has left, forms a protective cocoon around the boy. Calling on Askani, Cyclops asks her how she can save the child. She states she's from beyond and can save the boy's life. She also regrets that she won't be able to bring the boy back. Cyclops, torn between allowing his son to die and never seeing him again anyway, allows Askani to take him to whatever fate awaits him.
Later, as the Inhumans celebrate their victory, Cyclops and Charlotte Jones discuss his earlier choice. She thinks it seems so easily. He merely states that he has ideals, Xavier's Dream, and that helps him keep the big picture in mind. It's not easy, but hope is the ultimate motivator.
The Watcher concludes this arc with kind words for those who are willing to showing the noblest of qualities in being human.