Seeing Scott and Jean employ the use of their powers has reinforced Nathaniel’s theory of human evolution. Jean tries to advise Nathaniel against taking up Apocalypse‣s offer and return to a life with his wife and unborn child. Jean: “It’s never too late! We can change! We have a choice! It’s what makes us human!"
Meanwhile, Oscar gets attacked by Cootie Tremble, who has been transformed into a monstrous creation by Apocalypse. Jean goes to Oscar’s rescue, leaving Essex to ponder on the irony of Jean’s rescue in relation to the supposed theory of “survival of the fittest”.
Nathaniel: This woman...Risking her own life...To save the stinking hide of a lowly thief...How can that aid in her own survival? Could it be that in the future some of the mutated ones...Though a divergent species...Will remain in every way that matters, human?
Apocalypse has captured Scott and taken him back to his alien stronghold. Scott tries to break free of Apocalypse’s hold, but is overpowered; tied down, and his optic blasts inhibited, by Apocalypse’s techno-organic machinery. Apocalypse wishes to break his spirit to obtain the guarded knowledge that Scott possesses.
Nathaniel races back to the Milbury House in hopes of salvaging his marriage. He sees that the “freaks” he kept in his laboratory have been freed, by Rebecca as told to him by Daniel. He hears Rebecca’s cries and rushes to her bedroom. Their child is stillborn, and on her deathbed, Rebecca tells him she used to love and respect him, but his “genius” has made him “cruel” and “sinister”. She can never forgive him. Enraged, Nathaniel smashes all the tombstones in the Essex family cemetery, but he still can’t escape who he is. He then attempts to kill himself, pointing the trigger at his temple.
Apocalypse approaches the Hellfire Club in his disguise in an attempt to make use of their power in the world’s economy to cause “global upheaval and conflict” in order to “cull” the weak from the strong. Through “war and pestilence”, he’ll be able to “control those who would be born with the power to stand against [him]”.
Using her telepathy, Jean tracks Scott down to an old sewer by the River Thames. She finds Scott surrounded by mutated Marauders. In the course of trying to free her husband, she falls into a trap and ends up as a captive of Apocalypse as well.
A bedraggled Nathaniel Essex visits Charles Darwin. Nathaniel tells Darwin he has witnessed living proof that mutants exist.
Nathaniel: “The strong will be bad. The good, not strong enough. You and I, Charles, we have helped kill off the old Gods. But there will be new ones. And these Gods will be made in our own twisted image.”
Darwin thinks that the death of Rebecca and the child has driven Nathaniel hysterical. As Nathaniel leaves, he catches a glimpse of Darwin’s children. For a fleeting moment, he thinks of the children that could have been his, before his thoughts drift to Apocalypse.
Apocalypse muses over his success at having captured Jean by anticipating she’d never abandon Scott. And that is the weakness. Jean attempts a psionic attack but is counterattacked by Apocalypse. While Jean believes she has dissuaded Nathaniel Essex from joining Apocalypse, the latter shows up and agrees to serve Apocalypse in exchange to be freed of “morality and mortality”.
Several levels above Apocalypse’s stronghold, Oscar seeks the help of the “freaks” who have gathered to help free Scott and Jean. Daniel faith in Oscar helps the latter win the trust of the “freaks”. They attack the stronghold and free Scott and Jean while Nathaniel undergoes a transformation process which will turn him into Mr Sinister.