In the 853rd Century the original Superman still lives, but has spent over fifteen thousand years in a self-imposed exile in his Fortress of Solitude in the heart of our sun. The galaxy is protected by the Justice Legions, which trace their descent from the 20th Century Justice League and the 31st Century Legion of Super-Heroes, among others. Justice Legion Alpha, which protects the solar system, includes future analogues of Superman, Wonder Woman, Hourman, Starman, Aquaman, The Flash, Captain Marvel and Batman.
The original Superman announces that he will soon return to humanity, and to celebrate, Justice Legion Alpha travels back in time to the late 20th century to meet Superman's original teammates in the JLA, and bring them and Superman to the future to participate in games and displays of power as part of the celebration.
Meanwhile, in Russia, Vandal Savage, defeats the Titans single-handedly when they attempt to stop him purchasing nuclear powered Rocket Red suits. He then launches a nuclear strike on Washington D.C.
Unfortunately one of the Justice Legion (the future Starman) has been corrupted by Solaris, who has returned to his old habits. Before the original heroes can be returned to their own time, the future Hourman, an android, collapses and releases a virus programmed by Solaris to attack machines and humans.
The Virus affects the guidance systems of the Rocket Red suits and causes them to instead detonate over Montevideo, killing over a million people. The virus also drives humans insane, causing an increase in anger and paranoia worldwide. Believing this was deliberately planned by the JLA to stop him, Savage launches an all out war on superhumans using "blitz engines" he had created and hidden while allied with Adolf Hitler during World War II. The paranoia caused by the virus also leads the Justice Legion Alpha and the contemporary heroes to attack each other.
The remnants of the JLA that stayed in the present and the Justice Legion Alpha overcome their paranoia when the future Superman and Steel realize the significance of the symbol they both wear. The two JLA's are eventually able to stop the virus when it is discovered that it is a complex computer program looking for appropriate hardware. To provide this hardware the heroes build the body of Solaris (including in it a DNA sample of Superman's wife Lois Lane) and the virus flees from the Earth to this body, bringing Solaris to life. In a final act of repentance the future Starman sacrifices himself to banish Solaris from the solar system. The future Superman forces himself through time using confiscated time-travel technology he finds in the watchtower, almost dying in the process.
Meanwhile, in the 853rd century, the original JLA are fighting an alliance between Solaris and Vandal Savage. Vandal Savage has found a sample of Kryptonite on Mars (where it was left by the future Starman in the 20th century), which he gives to Solaris. Savage has also hired Walker Gabriel to steal the time-travel gauntlets of the 853rd century Flash (John Fox) to ensure the Justice Legion remains trapped in the past. However he ultimately double-crosses Gabriel.
Solaris, in a final attack, slaughters thousands of superhumans so he can fire the kryptonite into the sun and kill Superman before he emerges. The JLA's Green Lantern causes Solaris to go supernova and he and the Superman of the 853rd century contain the resulting blast - but not before the kryptonite is released.
The future Vandal Savage teleports from Mars to Earth using the stolen Time-Gauntlets. It turns out however that Gabriel has sabotaged the Gauntlets and Savage instead arrives in Montevideo moments before the nuclear blast he caused centuries earlier, finally bringing his life to an end.
It is then revealed that a secret conspiracy - forewarned by the trouble in the 20th century - has spent the intervening centuries coming up with a foolproof plan for stopping Solaris. Their actions included replacing the hidden kryptonite with a disguised Green Lantern Ring - with which the original Superman emerges from the sun and finishes Solaris.
In the aftermath the original Superman, who has become almost a god, and the future Hourman use the DNA sample to bring Lois Lane back to life. They also recreate Krypton, along with all its deceased inhabitants within our solar system. Lois and Superman apparently live happily ever after.