England, 1859. Rebecca Essex digs up the grave of her dead son. She suspects something of her husband, Nathaniel Essex. Something links his mad experiments with her son.
One month earlier, a pregnant Rebecca is digging in her garden and discovers a bone. Excited, she shows it to her husband, who is engrossed in his work, not wishing to be disturbed. He merely dismisses it as a fossil of a several million-year-old sea mollusk.
Rebecca: ’Forgive me, husband, but surely that is impossible. Father told me that Ussher worked out from the Bible itself that the world started only four thousand years before Christ.”
Nathaniel: “The Bible is wrong. There is no God. Though, if my theories are correct, some humans might -- in time -- evolve into Gods!”
Soon after, Nathaniel calls for a meeting of the Royal Society. Drawing upon Darwin’s theory of evolution, he goes on to explain further that humans have the ability to “undergo startling transformations” within the space of a few generations if the “offspring of certain racially superior individuals” were combined. These humans would “within a hundred years or so, mutate”. Nathaniel then unveils a monstrous creation, a body of a supersized human being with wings grafted onto him to present an example of a mutated human, of “human parts...fused...with anatomical regions of animals and other inorganic materials”. The council dismisses Nathaniel as a mad man, infuriated and driven by the loss of his son.
Darwin: “You cannot bring your son back. You cannot change the past by attempting to manipulate the future. Your work is in many ways breath-taking -- But you go too far.”
Nathaniel: “No! I must go further. I would if I could only free myself from this blasted so-called conscience that still pollutes me.”
Darwin: “But if you did...You would be a monster, sir. A monster, like your creation!”
Nathaniel: “If that is what is required for Science to progress...Then let me be a monster!”
Nathaniel gets drunk in a pub. There he meets Cootie Tremble of the Marauders, who offers to show him his collection of “creatures beyond [his] imagination...Freaks and fools and all types of misshapen folk.” Among the “freaks”, Nathaniel find a normal-looking dumb boy, Daniel, who hasn’t spoken a word since he witnessed the death of his parents. Nathaniel wonders why his son was born with ailments: Were they, too, part of nature's drive toward the future....Or simply cruel and pointless? Having seen too much, the Marauders threaten to kill him, but Nathaniel offers to buy their lot, encouraging them to join him in “the cause of Science”.
Two weeks later, the Marauders deliver Nathaniel’s goods to his house. Rebecca is suspicious of the equipment for her husband’s new experiment, but he tells her not to worry.
Meanwhile, Apocalypse arises from an ancient chamber buried beneath the city sewers. Apocalypse wonders through the “strange citadel called London”. He meets Tremble and his gang, who wants to capture Apocalypse as he will fetch a handsome price from Nathaniel Essex. Apocalypse demonstrates his power by killing one of the Marauders, and demanding the rest to serve him in exchange for their lives.
At the same time, in Westminster Abbey, a mysterious lady emerges from the brilliant light within the church. A disorientated Jean Grey has suddenly been brought back in time. Her husband Scott Summers, however, makes a less grand entrance in the sewers. He is also effectively blind without his ruby quartz visor.
Back at the Milbury House, an insomnatic Rebecca is plagued by the screams coming from her husband’s laboratory. She decides that for the sake of her sanity, she must know what lies beneath his “sacred place of work”. She finds a tank covered with sheets. She pulls it away to uncover her dead son preserved in the tank. A traumatized Rebecca runs to the grave where her son was laid to rest. She digs up the coffin, only to find it empty. Nathaniel finds Rebecca outside, and tries to explain that he merely wanted to “prevent others from dying like him”. But did this obsession lead to something more?
En Sabah Nur mysteriously appears at the gravesite, disguised as a noble man who expresses interest in his works.