A man narrates what has happened. He is on earth but a different one than he is from. On this one, Mutants took over led by Apocalypse. Humans did not go quietly and a long, bloody war took place.
Apocalypse was destroyed, but in his place came Weapon Omega. He was once Logan, a mutant who aided in the human resistance. He has been infected with the Apocalypse seed since and is intent on destroying the human race than Apocalypse, believing he has been charged with this task from the Celestials, omnipotent beings from the stars.
Weapon Omega and his Minister of Death, Azazel, stand in the bloody aftermath of a slaughter of the last enclave of man, the Vestry. Weapon Omega declares the age of man over and gives the humans credit for their tenaciousness. He says he was built for the fight not the victory but the coming battles with other mutants for evolutionary Supremacy would keep him busy. Azazel informs him of a celebration of the victory but Weapon Omega tells him to go. He has to find Jean Grey… his wife.
In a hovercraft, Jean Grey and Sabretooth talk to Bolivar Trask. Jean wonders if there were any survivors. Trask tells her there were 16,251 humans in the Vestry. He doubts there are half that many humans left in the whole world now. Jean tells Victor, Sabretooth, that she can’t feel any psychic signatures. Victor reminds her that both he and she have lost their powers and they are going to have to get used to it.
Trask tells Victor that he is under arrest. Jean is appalled. Prophet, William Striker aka Prophet enters and says Victor is lucky because all other former Apocalypse Hounds were killed on sight and he is being allowed to live. Prophet promises that Victor will be treated fairly due to his assistance to the human resistance. Victor says he knows he should pay for his past crimes but he is not going in a cell and he does not trust his life with Prophet and Trask.
Victor attacks Prophet but is easily subdued. Prophet explains that he has studied Victor’s fighting style and it is dependent on his healing ability. Prophet suggests he should learn some defensive maneuvers.
At the humans’ base Trask tells his daughter Francesca, A.K.A. Fiend, to be careful. Fiend is a member of Prophet’s team and an expert with a blade. Prophet tells Trask that he and his team will be gone for a few months. Fiend informs Jean that Victor will be okay and that Prophet believes mutants and humans are the same. Prophet tells Jean that she could use the time to discover that her lost powers were the least of her talents. Jean asks what his plan is and he replies “…To kill your husband.”
In New Apocalypse, formerly Manhattan, the narrator describes that the “haves” live in gleaming towers whereas the “have nots” live in the dregs and are forced to register their powers to see how they can be used. One of the clerks is Zora Risman, A.K.A. Deadeye. Deadeye is another member of Prophet’s team “—Whose photographic memory is only surpassed in sharpness by her aim.”
In a night club in the Dregs, Greydon Creed is trying to pickup a mutant girl when he gets a text that says “COFFEE!” He orders a lot of coffee because the text meant he is being called by Prophet to join the team as Horror Show.
At the Hellfire Club, Donald Pierce is beating his fellow members at cards when he too gets a text with a girl’s name on it. He excuses himself from the game and his present company which he secretly despises and goes to join Prophet's team as Goodnight.
People are rioting in the Dregs due to a pamphlet that has been published comparing humans to mutant and showing that they are the same. Watching from above is Prophet’s team, The X-Terminated. Prophet reads from the pamphlet and tells his team they are there to save the author. Through his pamphlet he has caused more of an uproar in the people in a few days than The X-Terminated have done in two years. Therefore he has been marked for execution.
The narrator reveals the author of the pamphlet is him. His name is Harper Simmons; he is a reporter in his reality of earth. He is serving soup when Keeper Murdock, known as Daredevil in Simmons’ reality, stops the soup line and demands Simmons steps forward or every third person in the line will be killed.
Murdock points to one man and orders him to be killed when Simmons steps forward. He is shot with a tranquilizer dart and The X-Terminated attack Murdock and his men. They are able to save Simmons and get away before the Samurai Sentinels arrive, but “They say once the keeper has heard your heartbeat you’re his forever.”
Once Simmons wakes up, he tells them he is from another Earth. He was investigating a prison break of the mutant Dark Beast by Sugar Man and found their secret lab. They returned while he was poking around and opened a portal. They went through the portal and set the lab to explode. Simmons’ only escape was through the portal.
Prophet asks Simmons to take him to where he came through the portal as it could give them some knowledge. Simmons takes them to an abandoned work dispensary. Prophet’s sensor picks up power readings behind a wall. Fiend opens the secret door only to find Weapon Omega’s men being led by Cyclops…..