As the film opens, Superman has already died at the hands of Doomsday. The last remaining Monitor retrieves Superman and brings him to what is left of where the Monitors watched over the Multiverse. He explains the nature of reality to Superman. Each Universe is watched over by a Monitor and there are far more than his own. Superman, incredulous, looks into the Multiverse laid out in front of him. Superman sees a man smiling across from a beautiful brunette woman at an outdoor cafe. He asks the Monitor who that is, to which the Monitor replies that it is Bruce Wayne (This is the end scene of Dark Knight Rises). Superman, taken aback, says, "But...he looks so happy..." "Not the Bruce Wayne of your Earth, Kal-El"
The Monitor explains to Superman why he was brought here. When Superman killed Zod on his Earth, it corrupted that Universe's Monitor. That Monitor has now become an Anti-Monitor, who is attempting to collapse the entire Multiverse and destroy all of existence. He explains his Earth is at the center of everything. The Monitor tasks Superman with confronting the Anti-Monitor and redeeming himself and reality itself.
Meanwhile on one of the Earth's, we see an older Batman (from Tim Burton's films) running across the rooftops. Suddenly something catches his sight and with a piercing boom Batman is shot and falls to his death. Orion appears before The Justice League to warn them of the threat of Darkseid and his pursuit of the Anti-Life Equation, asking for their help in locating Scott Free. What they do not realize is Darkseid has already acquired both Scott Free (aka Mister Miracle) and the Anti-Life Equation. The actions of the Anti-Monitor have caused enough damage in their Universe to give Darkseid the advantage and unleash hell on Earth.
Darkseid invades Earth and begins rounding up superheroes and using the Anti-Life Equation. The remaining members of the Justice League make a final stand in Metropolis against Darkseid's army when suddenly Superman returns with reinforcements. While the events on this Earth were unfolding, Superman traveled the Multiverse, recruiting Supermen and others from various Universes to help defeat Darkseid. Darkseid fires his Omega beams at Superman in the final confrontation, with Mister Miracle throwing himself in front of him and sacrificing himself. In that moment the Supermen dispatch Darkseid.
The film ends with Scott Free cheating death and breaking out of his grave.