Crisis on Infinite Earths

The conflicting stories of the DCU are explained as a Multiverse, containing many parallel universes and alternate versions of the characters, with the primary DC continuity referred to as Earth-One. They were created after renegade scientist Krona built a machine and used it to look back into the beginning of time. A cosmic being from the beginning known as the Monitor catalogues these realities, but he has an evil counterpart, the Anti-Monitor, who comes from an antimatter universe. After Pariah causes an accident with antimatter in his universe, the Anti-Monitor is released and begins destroying many of the realities with a wave of antimatter, planning on becoming sole ruler of all realities. On Earth-Three, Alexander Luthor and Lois Lane teleport their son Alexander Luthor Jr. to another reality as Earth-Three is consumed by the antimatter wave. To combat this, the Monitor recruits heroes and villains from across time and space to set up five towers, to help merge the multiverse back into one to make it stronger.
The Monitor dispatches a team of heroes across time and space to defend mysterious machines that could be the key to saving the remaining universes. Meanwhile, it is revealed that the Flash was transported to the future, and Pariah, constantly witnessing the destruction of worlds, arrives on the doomed Earth-1.
Barry Allen of Earth-One encounters the antimatter wave before being captured by the Anti-Monitor. On Earth 1, various heroes attempt to save people from the approaching antimatter wave. During WWII, the Monitor's towers appear during a battle in which Sgt. Rock, Haunted Tank, and the Losers are fighting together against Nazis.
The Monitor gives powers to Kimiyo Hoshi, turning her into Doctor Light. He is murdered by Harbinger, who is possessed by one of the Anti-Monitor's shadow demons. However, the Monitor knew this would happen and his death releases enough energy to project two of the last five parallel Earths into a protective limbo that nullifies the wave. 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 then recruits heroes from the remaining Earths to lead an assault on the Anti-Monitor in the antimatter universe, using the powers of Alexander Luthor Jr., the last survivor of Earth-Three, 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, used to destroy the last five Earths; the injured Anti-Monitor retreats and Supergirl dies from his attacks after a distraction from Hoshi. The Anti-Monitor creates a new body for himself and tries to use an antimatter cannon to penetrate the limbo universe and destroy the five partially merged Earths. The Flash dies stopping this attempt by using his speed to channel energy.
During a lull in the war, the villains unite under Brainiac. He kills Earth-Two's Alexei Luthor while recruiting the Earth-One Lex Luthor to conquer the remaining Earths. A furious Anti-Monitor absorbs the energy of millions of worlds and 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 planet Oa to prevent 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 Alexander Luthor Jr. 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 who kill Dove, Lori Lemaris, Green Arrow of Earth-Two, Prince Ra-Man, Clayface, Bug-Eyed Bandit, Kole, Huntress, Robin, Sunburst, and Ten-Eyed Man. He falls in a carefully-planned counterattack, culminating in a battle with Superboy of Earth-Prime, Kal-L, and Alexander Luthor Jr., with help from Darkseid. In this final battle, the Anti-Monitor, reduced to a flaming head, crashes into a star and is killed by Kal-L. Before the star explodes, Alex sends Kal-L, Earth-Two Lois Lane, Earth-Prime Superboy and himself to a pocket "paradise" dimension while Wonder Woman of Earth-Two is taken to Mount Olympus by Zeus. This leaves the heroes of the remaining Earth, none of whom remember the original past, to sort out the aftermath of this crisis. Only Psycho-Pirate, who is locked up in Arkham Asylum, remembers the multiverse.