The conflicting origins and stories of the DC universe are explained as a Multiverse, containing many parallel universes and alternate versions of the characters, with the primary DC continuity referred to as Earth-1. A cosmic being known as the Monitor supervises many of these realities, but is opposed by his counterpart the Anti-Monitor, who comes from an antimatter universe and begins destroying many of the realities with a wave of antimatter, to replace them with his own.
The Monitor is murdered by his protege, Harbinger, who is possessed by one of the Anti-Monitor's demons; his death releases enough energy to project the last five parallel Earths into a protective limbo. The Anti-Monitor recruits Psycho-Pirate to his cause, infusing him with part of his power to manipulate the heroes of Earth-4, Earth-S and Earth-X against the rest; this fails when all five Earths enter the limbo universe. Harbinger recruits heroes from the remaining Earths to lead an assault on the Anti-Monitor in the antimatter universe, using Alexander Luthor, Jr.'s powers to open a portal between the limbo and antimatter universes. Pariah tracks down the Anti-Monitor at his fortress, and the heroes destroy a converter powered by stellar energy to destroy the last five Earths; the injured Anti-Monitor retreats and Supergirl dies.
During a lull in the war the villains unite under Brainiac, who kills Earth-Two's Alexei Luthor while recruiting the Earth-One Lex Luthor to conquer the remaining Earths. The Anti-Monitor tries to use an antimatter cannon to penetrate the limbo universe and destroy the five partially merged Earths. The Flash (Barry Allen) dies stopping this attempt. A furious Anti-Monitor vows to travel back through time to prevent the creation of the multiverse. The Spectre unites the heroes and villains by warning them about the Anti-Monitor's plan; the heroes travel back in time to stop the Anti-Monitor, while the villains travel back in time to the ancient planet Oa to prevent renegade scientist Krona from creating the technology necessary for the Anti-Monitor's plan to succeed. The villains fail, and Krona continues his experiment. The Anti-Monitor waits for Alex Luthor to reopen the portal between the positive and antimatter universes, capturing the heroes, but a magically empowered Spectre creates an energy overload which shatters space and time. The five Earths merge into a single shared universe, and the superheroes return to the present; only those present at the dawn of time remember the original realities.
A cosmically empowered Anti-Monitor attacks again, transporting the new Earth to the antimatter universe and summoning a horde of shadow demons. He falls in a carefully planned counterattack culminating in a battle with Kal-L (the Earth-Two Superman), Alexander Luthor of Earth-Three and Superboy of Earth-Prime, with help from New Gods adversary Darkseid. In this final battle the Anti-Monitor, reduced to a flaming head, crashes into a star and dies. As they are the only four who remember the original past, Alex sends Earth-Two Superman, Earth-Two Lois Lane, Earth-Prime Superboy and himself to a pocket "paradise" dimension.
Possible alternate ending
According to George Pérez in a Wizard magazine interview in 1994, Chris Claremont suggested that Superman of Earth-One dies in the final battle with the Anti-Monitor in issue #12. After the Anti-Monitor was destroyed for good, Kal-L from Earth-Two realizes that he is now alone, without his Earth, without his Lois, and now the new single Earth is without a Superman. Then he remarks, "Don't need this anymore," and brushes the white dye off his hair and other make-up that he apparently used to make himself look aged. The other heroes are surprised by this and Kal-L simply explains that he had stopped aging when he reached the peak of his powers. He returns with the other heroes to the new post-Crisis Earth, taking the place of the Earth-One Superman.
If this idea had been used, then The Man of Steel would have marked the return of the "Original Super-Hero", as Kal-L (now switched to Kal-El) begins his life on the post-Crisis Earth, which is similar to his old life, but with distinct differences. Despite this "culture shock," Kal-L endures and is given a new lease on life by being deposited back to the early days of the modern heroic age of the post-Crisis Earth. However, this was discarded when the John Byrne version of The Man of Steel was planned.
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