Across the multiverse, Captain Marvel of Earth-5 and Renee Montoya work to recruit the greatest heroes of the 52 to save existence from the entity threatening the multiverse.
In Command-D, Superman holds Batman’s corpse, as Darkseid mocks Superman for failing to defend Earth, and that as Darkseid has becoming everyone and everything, Superman is now the enemy of all that lives. Driven to a rage, the Man of Steel is about to tear the Dark God apart when he realises that Darkseid is in Dan Turpin. His hesitation allows the Anti-Life infected slaves to surround Superman. Darkseid declares that the Final Crisis is over, and he has won, preparing to fire the Radion bullet which will kill Orion in the past. Speaking through Turpin and his Anti-Life slaves, Darkseid asks if Superman will join Batman in the Omega Sanction, or try and outrace it. Superman refuses to give into Darkseid and tells him its not over yet. Just then, Barry Allen and Wally West arrive, leading the Black Racer to the dying Darkseid. The Anti-Life slaves unleash Omega Beams on the two Flashes, who outrace them, run past Superman (who is naturally surprised by Barry’s presence) and vibrate through Darkseid. Having just fired the Radion bullet, Darkseid panics at the sight of the Black Racer, who claims Darkseid’s soul, removing him from Turpin’s body.
At Checkmate Castle, the Atoms manage to establish a tunnel to another Earth in the Multiverse. However, the stress is far too much for Lord Eye to handle. Additionally, the Justifiers break into the Castle. The OMACs under Mr. Terrific’s command are not enough to stop the Justifiers, and Mr. Miracle’s motherboxx opens a boom tube to the planet that Checkmate had selected for escape. Unfortunately, their choice of world was poor, as the Checkmate survivors end up on Earth-51. Fortunately, Captain Marvel and the Ultima Thule showed up, and he informed them of Superman’s plan to gather the Supermen. Renee joins Marvel on his quest, informing Overman of the death of his cousin.
Back on New Earth, Superman is almost amused by the irony of the situation: by firing the bullet to kill Orion, Darkseid insured John Stewart discovered the bullet, which would make its way into Batman’s hands, and be used against him. For all intents and purposes, Darkseid committed suicide. the Female Furies, lead by Wonder Woman, arrive to avenge their master. Superman is horrified at the sight of his best friend enslaved by Darkseid, and Wonder Woman tells Superman that he is outnumbered, as Libra’s army of mind-controlled superhumans arrive. However, the Secret Society are now under the control of Lex Luthor and Doctor Sivana. Frankenstein and Supergirl lead the remaining free heroes to the battle, and overwhelm the Furies. Frankenstein is able to free Wonder Woman from the Anti-Life Equation, and she binds Darkseid with the Lasso of Truth, freeing the rest of humanity from Darkseid’s control.
As reality breaks down around him and the Earth slowly dies, Superman begins construction of a copy of the Miracle Machine, while Supergirl and Wonder Woman begin shrinking down and cryogenically preserving the people of Earth. Lois Lane, Jimmy Olsen, and Supergirl send a rocket through time as a time capsule, containing mementos of their Earth in case the Miracle Machine doesn’t work. Once all of humanity is preserved, the last remnant of Darkseid’s mind appears to try and claim the Miracle Machine, but Superman is aware that Darkseid’s essence vibrates like the multiverse does, and shatters his vibrational frequency with a single note.
Finally, the Miracle Machine is ready. All Superman needs is a piece of Element X, the fire of the Fourth World, to power the machine, which he can use by activating the Moebius Chair. Just then, Mandrakk the Dark Monitor arrives to consume all remaining life, saying that Superman has nothing to power the chair. To Mandrakk’s shock, Superman instead uses the solar energy in his body to power the chair. At the same time, an army of alternate Supermen from across the Multiverse, led by the Captain Marvel of Earth-5, arrives, followed by Nix Uotan who, in turn, summons the Zoo Crew (restoring their original forms and powers in the process), the army of Heaven, the Green Lantern Corps, and the Super Young Team (now transformed into the new Forever People). The battle ends when Hal Jordan directs the Green Lantern Corps to stake Mandrakk with a spear created by their rings.
Superman then wishes upon the Miracle Machine for “a happy ending”, recreating the Multiverse as it was before Darkseid’s ascension. Following this, Superman and the Green Lanterns begin repairs to the Orrery. Nix Uotan gives a report to the Monitors on these events, and that the New Gods of New Genesis will travel to Earth-51 to restore life to it. Nix then reveals that he used the Miracle Machine to erase the Monitors from existence and turn himself into a human being, believing that the Monitors have become too detrimental to the Multiverse to continue. Before they fade, Nix Uotan shares his last moments as a Monitor with Weeja Dell, telling her that he could never forget her.
In the distant past, Anthro dies of old age after bringing fire to the people of Earth. Bruce Wayne, still in his Batman garb, lays his utility belt upon Anthro’s body, and starts drawing a story on the cave wall.