In the rather bleak future of “Kingdom Come,” a new breed of super powered being has made life very unpleasant on Earth. Ultimately, Superman is forced to come out of his self-imposed retirement to bring order to the world once more.
He and the remaining superheroes slowly begin to collect the various super powered thugs and criminals and start housing them in a prison designed to house super humans. Superman makes the hero Captain Comet warden of the prison, which soon begins to take on the nickname "The Gulag."
Meanwhile, Batman has infiltrated Lex Luthor's Mankind Liberation Front, where Luthor has a now-adult Billy Batson under his control due to mind-controlling worms in Billy's ear. Batman manages to take Luthor out of the picture, but not before Billy escapes.
The situation at the Gulag is deteriorating rapidly – as more and more prisoners are showing up, a riot appears inevitable, and eventually the inevitable takes place and Captain Comet is murdered. Superman and the Justice League show up to put the riot down, and Superman convinces Batman to help, as well, with his group of mostly non-powered heroes. At this point, though, Superman and Wonder Woman clash, as she wants to use deadly force, which Superman is not willing to use. This leads into the last issue, “Kingdom Come” #4.
The heroes of the Justice League (along with Batman's legions) clash with the escaped convicts, and two other factors enter the picture to make things even worse. First, Billy Batson finally says his magic word, "Shazam," and enters the fray as Captain Marvel – matched up with Superman. Second, the United Nations has decided to write superheroes off, and has authorized the use of three planes carrying nuclear bombs to be dropped on the Gulag to end the matter once and for all.
After a confrontation against each other, Batman and Wonder Woman team-up to each take care of one of the planes.
Superman, meanwhile, is having a hard time with Captain Marvel, who is saying the magic word constantly, each time bringing down magical lightning which he is using to assault Superman, whose weakness is magic. Their battle is interrupted when the last of the nuclear bombs is actually dropped. Superman argues with Captain Marvel, trying to get to Billy inside, telling him that it must be up to Billy to determine what happens with the bomb, as Superman cannot decide whether the bomb actually should be allowed to drop on them all. Finally, Billy breaks free of his controls and flies off to the bomb and, for the last time, calls down the magic lightning and detonates the nuke in the sky.
While the bomb still kills a number of the people below, Billy manages to save a great deal of the super humans, who have stopped fighting due to the blast.