The only person who refuses to believe that Superman is dead is Batman. He analyzes the evidence from the battle, insisting that objects can't disappear without a trace, citing the law of conservation of mass. He snubs the invitations of Alfred and the other Leaguers to attend Superman's funeral in Metropolis.
At Superman's funeral, the attendants include the League (minus Batman), the staff of the Daily Planet, Jonathan and Martha Kent, several Earth leaders, and superheroes. However, everyone gasps as Lex Luthor arrives. Lois Lane is furious that Lex has appeared as she believes him to come to gloat over Superman's death, she soon breaks into tears until Lex comforts her and genuinely admits that he will also miss Superman greatly.J'onn J'onzz pronounces a eulogy and the League ceremonially inters a coffin in a monument. As they bring the coffin to his memorial, Wonder Woman spots Batman watching the procession from the shadows.
Holding a wake for Superman in the Watchtower, the League swaps stories about him, then J'onn tentatively proposes adding a new member. Suddenly, Lobo crashes through the window, announcing that he's there to take Superman's place. When the League orders him out, he decides to "audition" by tearing the Watchtower apart and attacking them. They hold him off, then hear that dozens of supervillains are running amok in Metropolis, celebrating Superman's death in their own fashion. The League reluctantly bring Lobo along as they go to fight, mainly because they don't trust him alone in the Watchtower. However, given his unique fighting ability, they allow him to join the battle, only as long as he follows their direct orders.
Investigating another of his theories, Batman follows a trail to Superman's memorial. Finding nothing, he wonders if he's wrong and Superman really is dead. Alone, he takes this opportunity to tell Clark that, despite their differences, he has always respected him and what he taught him and that he will miss him... but his tribute is interrupted by a nearby explosion, and takes off to battle the attacking supervillains.
The League attacks, with difficulty subduing the rogue villains. Lobo makes himself useful in his own fashion, beating Kalibak into submission with a few cars forcing him to say Uncle and causing plenty of destruction in the process. To an already grieving League, Lobo boasts how with him on the team, Superman is no longer needed. The Leaguers bow their heads, contemplating life without the Man of Steel. Elsewhere, on a barren landscape, under a red sun and some rubble lies... Superman.
Superman regains consciousness and sees the barren landscape, as well as a few sections of Metropolis that were hit by Toyman's disintegrator beam. Wherever he is, the beam transported him there instead of destroying him. He sees that the sun is red, meaning his powers will wane. Also, his communicator does not have any audio. He picks up a signal on the communicator and decides to move closer to it. Salvaging what food and supplies he can from the cars in the street fragments, he then siphons gas into one of them and drives off.
Unable to find anything else, he makes camp one night and is menaced by a pack of wolf-like creatures. He manages to drive them away with fire. To prepare for any more dangers that lie ahead, he uses the last of his heat vision to fashion an iron bar into a crude-but-effective sword. Before too long, his car is out of gas and he is forced to walk. Attacked that night by the creatures again, he kills their leader and subjugates the rest of the pack, harnessing them as sled dogs for a new improvised vehicle and wearing the leader's pelt.
After a few more days, he reaches the ruins of a city and finds the source of the signal: the Watchtower, crashed to the ground. Entering, he tries to access its computer. It tells him that the rest of the League's whereabouts are unknown, then shuts down due to low power. Superman bangs his fists down in frustration and asks aloud, "What happened to everybody?" A voice answers, "They died, Superman. Thousands of years ago." A figure appears from the shadows... Vandal Savage.
Savage seems uncharacteristically glad to see Superman and he soon explains why: the planet they are on is Earth, 30,000 years in the future and the entire human race, except for the immortal Savage, is dead, meaning that the whole Earth belongs to him now.
Savage explains that, only a few months after Superman disappeared, he developed a weapon that allowed him to control the force of gravity. Without Superman, Savage killed the rest of the Justice League and proclaimed himself ruler of the Earth. But his newfound powers disrupted the balance of the solar system, killing the rest of the human race. Superman is initially enraged, but Savage says he's reformed: after millennia of loneliness and isolation, he's come to realize that his obsession with power was meaningless.
With plenty of time on his hands, Savage has built himself a luxurious mansion in the ruins of Metropolis, with a large garden and plenty of technological amenities. He passes his time reading, working on various inventions, or on hobbies such as restoring other parts of the city. One of them includes a spaceship that he intended to use to explore the universe, but chose not to as penance for his previous misdeeds. He treats Superman to a home-cooked meal and invites him to stay. Wandering around the mansion one night, Superman finds a time machine. He asks Savage why he did not finish it. Savage says there would be no point, as the machine would not allow him to travel back to any time where he was already alive. Superman points out that he can, since he's dead and can stop Savage's destruction of the Earth.
He and Savage work together to complete the machine, but find that they can't keep the portal open without a much larger power source. Savage knows of only one: a zero-point energy generator that he built, but was stolen some years ago by a colony of giant cockroaches. Since Savage stated that building another one will take fifty years, he and Superman sneak into the colony to get it back. In battle with the roaches, Superman apparently falls to his death into the pit containing the generator – but instead, the device, which, as Savage has explained, is like a "miniature sun", instantly restores his powers and he is able to get himself and Savage away safely.
Savage opens the portal, giving Superman the information he needs to thwart his younger self's plan. Before going, Superman asks what will happen to Savage if he succeeds. Savage says he may be possibly redeemed but tells him not to worry. The two men shake hands and Superman departs.
Back in the present, while Lobo is crowing over Kalibak, Deadshot takes aim at Batman with a missile. Superman's hand appears and catches it. In wonder, the League crowds around him (except for Batman). Superman tells Lobo he's fired and the bounty hunter angrily jets away on his bike. Superman says he'll explain what happened to him, but first they have a job to do. The League flies into action, with Superman leading the way.
In the future, Savage is sitting alone among the ruins of Metropolis. He sees a ghostly figure of a child run by, then more people. Slowly, the ruins disappear and a living city replaces it, filled with people. Savage sees his own body becoming translucent and says, "Thank you, my friend..." before fading into the new timeline.