In Brainiac's starship, Dolphin, Captain Comet, Rip Hunter, Animal Man, the Atomic Knight, and Adam Strange convince the reviving robot that his memory was tampered with to make him forget the Crisis. Admitting that his power is inadequate to battle the Anti-Monitor, he sets course for the world of a more powerful being. On Earth, the Anti-Monitor's visage is seen in the skies all over the globe. He repeats that the Earth is now in the anti-matter universe. His past victories over positive universes are meaningless, he says, because of the super-heroes' efforts to stop him. When he lists Supergirl and the Flash as casualties, Kid Flash demands to know what has happened.

The Supermen scan the globe and watch the populace panicking. Harbinger appears, and teleports them to a chosen destination, then gathers Dr. Light from Japan, leaving Sunburst to defend the island. When Dr. Light states that she caused Supergirl's death, Harbinger replies that the battle had already killed Supergirl, and that the Anti-Monitor's final attack merely gave her a swift death. In the skies, the darkness splits into a million shadow demons, which begin an all-out attack on humanity, and the super-heroes mass to resist them. The Global Guardians team with other heroes to free their native lands from the threat, but the demons' numbers seem endless. The Phantom Stranger summons Dr. Mist to help revive the Spectre who lies comatose. Below, Harbinger has gathered a large group of heroes, along with Pariah and Alex, to lead a final assault on their nemesis. Alex creates a bridge between universes, and they depart near Apokolips.

Brainiac's ship goes into stationary orbit, and he and his guests teleport to the planet, where Darkseid appears and introduces himself.

Back on Earth, the majority of the heroes are still battling the demons. The Dove is slain by a shadow-being as his brother watches in horror.

In Dr. Fate's Salem tower, the magically powered heroes have gathered to pool their shamanistic might. The Earth-2 Green Lantern and Dr. Occult form the nexus of their energy.

On Qward, in the anti-matter universe, Harbinger and the heroes have arrived in the Anti-Monitor's old headquarters. Kid Flash insists on joining them because of his mentor's demise. Suddenly, an image of the Flash appears to him—the last one Barry cast before his death. Wally follows the afterimage to where an insane Psycho-Pirate clutches at an empty uniform. Kid Flash knocks him out, and realizes that Barry Allen is truly dead when Lady Quark finds his ring. Pariah informs them that a great concentration of evil lies before them. They follow to find a towering Anti-Monitor, ready for the final slaughter.

In Atlantis, Aquaman leads his underwater legions against the shadows. Lori Lemaris saves a trapped Mera with a force beam. A demon closes in on her and kills her. In Chicago, Green Arrow of Earth-2 is killed by a shadow. In Philadelphia, Cyborg, the Son of Vulcan, the Vigilante, and the New Wildcat continue rescue operations.

In New Orleans, Shade the Changing Man witnesses the death of Prince Ra-Man. In Skartaris, Travis Morgan leads his forces against the black menaces. In Gotham City, both Clayface II and the Bug-Eyed Bandit perish at the hands of the demons. In Salem, the tide finally turns. The supernatural crusaders send their combined force in a net of energy to gather the demons from the Earth's surface, and bind them helpless in space. Over the Earth, lives have been lost, including those of Kole, Huntress, and Robin, but other lives have been saved. For a moment, the survivors can take stock.

On Qward, the Supermen of Earth 1 and 2, Captain Atom, Lady Quark, Firehawk, Wonder Woman, and other tarot's strike at the Anti-Monitor, but he ignores their blows, feeding on the energy of a nearby star, As Dr Light absorbs the energy of one of the binary suns they are between, the Anti-Monitor feels his power draining away. Alex begins to drain the anti-matter energy away from their enemy. Negative Woman uses her negative-self to bind the Anti-Monitor and inhibit him: then Harbinger leads all the energy-producing heroes against him, Dr. Light blasts him with the energy of a sun, and he falls into the ruins of his fortress. Alex creates a dimensional hole, large enough to enclose the Earth and return it to its proper universe. The heroes follow. The ball of bound demons hover and then fall on the fallen enemy. Thus, the Anti-Monitor absorbs his slaves energies and rises again, while the heroes start to give battle. Wonder Woman is caught in a withering flash of power, and is borne away to an unknown destination. Superman of Earth-1 and Lady Quark vow deadly revenge, but Kal-L knocks them out, and tells Superboy to take them back. Since he has no world and no wife to return to, the elder Superman has the least to lose. Then he confronts the monstrous Anti-Monitor, and batters him. Superboy sends Superman and Lady Quark back through Alex's shrinking body, and turns to aid him. Superman continues his one-man war against the Anti-Monitor, striking telling blows, while the villain, his power waning, absorbs more energy from the anti-cosmos, and blasts him and Superboy. Darkseid, watching the conflict on a viewscreen, proclaims his planet to be endangered if the Anti-Monitor survives, sends a power burst at him through Alex's eyes. The enemy, devastated, is hurled into the core of one of the binary suns. Superman, Superboy, and Alex are stunned to see the spectre of their enemy rising from the sun. Superman smashes into his foe's fiery body, scattering him: the remains fall back into the sun and the star begins to implode.

They bravely await the end and Superman wishes that Lois could have lived to see their triumph. At that, Alex produces Lois from a void-pocket in his body where she had been sent to wait. She tells her husband that she had been to a tranquil world. Alex cannot return them to Earth but he can take them all to this beautiful world. Superman, Lois, and Superboy opt for that choice. The foursome vanish seconds before the exploding sun would have reached them.

Back on Earth, Lyla is explaining facets of the Crisis to Pariah and Lady Quark. Wonder Woman was returned to the clay which Aphrodite and Athena had given life, then spread across Paradise Island.

Time then continued to reverse itself, as the Amazons were returned to their original homeland before they fled Man's World. Zeus brought the homeless Wonder Woman of Earth-2 and her husband Steve Trevor to Olympus, where they could live peacefully. The bodies of Robin of Earth-2, the Huntress, and Kole were never found. All those who died were mourned. In Keystone City, Jay Garrick determined that Kid Flash's illness was in remission, his body chemistry being changed by a blast from the Anti-Monitor. He could again move at super-speed, though only to a maximum of Mach-1. Wally donned Barry Allen's uniform, and announced, "From this day forth — the Flash lives again!"

The Great Disaster will not exist in the Earth's future, but a lost child will he found in Command D. adopted by General Horatio Tomorrow of the Planeteers, and named Thomas. Jonah Jex will be torn from his era to fight in the future, while the Guardians of the Universe must face the first division in their ranks. Thus, Lyla concludes her tale, and Lady Quark and Pariah ask her to help them explore their new homeworld. They leave with her, honoring the memory of their benefactor, the Monitor. And, in Arkham Asylum, the staff discuss a new patient who seems beyond help, straitjacketed in a rubber-lined room. Roger Hayden, formerly Psycho-Pirate, gibbers about Earths beyond numbers, the Anti-Monitor, and the memories, which only he had been allowed to keep.