The time-travelling villain from Earth-2, Per Degaton, sought revenge on the various super-hero teams that had defeated him in the past: the Justice Society and the All-Star Squadron. While travelling the limbo between worlds, Per Degaton noticed an emerald prison. Upon closer inspection, Degaton discovered the Crime Syndicate of Earth-3, imprisoned by Green Lantern after their most recent fight with the Justice League and Justice Society. Per Degaton freed them and enlisted them in his plans for revenge. Degaton picked the perfect time to strike: during the annual meeting between the JLA and the JSA.
Once every year, the JSA transported to the JLA’s base of Earth-1 (or vice-versa) to meet. This time, however, the JLA ( Aquaman, Firestorm, Hawkman, Superman, and Zatanna) did not receive the guests they expected. Instead of the JSA, they encountered the Crime Syndicate. While the JLA and the Crime Syndicate fought on the Justice League Satellite, the JSA found themselves transported to another world, Earth-Prime. However, unlike the normal Earth-Prime they anticipated, they found themselves in a nuclear holocaust.
Prior to freeing the Crime Syndicate, Per Degaton had discovered Earth-Prime. He and the Crime Syndicate returned there, to its year 1962. Once there, Degaton made use of the Cuban Missile Crisis to not only steal a ton of nuclear weapons but to also bring the crisis to its head. The resultant nuclear war between the U.S. and U.S.S.R. destroyed the planet. Now, the Justice Society ( Doctor Fate, Green Lantern, Huntress, Power Girl, and Starman) found themselves trapped in a post-apocalyptic world, filled with mutated threats. The Justice League is temporarily defeated by the Crime Syndicate, who flee the JLA Satellite in a space shuttle. The JLA does not pursue, but rather head to Earth-2 to find the whereabouts of the missing Justice Society. They travel to Earth-2 to find the world has been conquered by Per Degaton.
The JLA discover that Per Degaton and the Crime Syndicate had taken the stolen Cuban Missile Crisis missiles back to 1942, where he used them to blackmail the world and take control, thereby altering history. The Justice League travel back to Earth-2’s 1942, where they encounter the All-Star Squadron ( Commander Steel, Firebrand, Johnny Quick, Liberty Belle, and Robotman). The heroes compare notes and are soon witness to Per Degaton’s threats: unless the nations of the world surrender to his rule, Per Degaton will detonate the atomic bombs he has stolen from 1962. Degaton promises a show of force by detonating one of the bombs, and the heroes rush to prevent his plan from happening.
Back on the post-apocalyptic Earth-Prime, the JSA realize what has happened in its past. Doctor Fate’s magic reveals that Per Degaton is behind the destruction of Earth-Prime, and they follow his path to Earth-2’s 1942 to stop him with the stolen missiles. The JSA appear alongside the JLA and the All-Star Squadron, but the heroes are too late to stop Degaton from exploding one of the nuclear missiles.
The three teams use their powers to find multiple locations where Per Degaton has planted the missiles. They split up into teams but finds each site is guarded by a member of the Crime Syndicate. The heroes, though, outnumber each Crime Syndicate member three-to-one and defeat each Syndicate member. The heroes close in on Degaton, and, with the missiles destroyed, stop him from carrying out his threat. Zatanna, Green Lantern, and Firebrand travel to 1962 on Earth-Prime and prevent Per Degaton and the Crime Syndicate from stealing the missiles, to begin with. This prevents Per Degaton from carrying out any of his plans, and Zatanna and Green Lantern use their combined powers to return Degaton to his past with no memory of his plans. With history now rewritten, each hero and villain returns to their original place in time and space, not even aware that this event happened.