In the 1950s, the Soviet Union reveals its newest asset to be Superman. The sudden revelation of a superpowered alien under Soviet control causes panic in the United States, shifting the focus of the Cold War arms race from nuclear weapons to superhumans. CIA agent Jim Olsen recruits Lex Luthor, a scientist employed by S.T.A.R. Labs, to destroy Superman. Luthor's first act is to cause Sputnik 2 to plummet towards Metropolis. After Superman diverts the satellite away from the city, Luthor retrieves his genetic material and creates a clone of Superman named Bizarro.
Meanwhile, Superman meets Wonder Woman at a diplomatic party, and she becomes smitten by him. Pyotr Roslov, the head of the NKVD and Joseph Stalin's illegitimate son, is angry that Superman has turned his father's attention away from him and ended his chances of advancement within the Soviet regime. Pyotr shoots a dissident couple in front of their son for printing anti-Superman propaganda. Stalin dies from cyanide poisoning, and Superman initially refuses command of the Communist Party. However, a chance meeting with Lana Lazarenko, his childhood sweetheart, changes his mind. Superman chooses to use his powers for the greater good and turn his country into a utopia.
The U.S. government sends Bizarro to engage Superman, and their duel causes an accidental nuclear missile launch in Great Britain. The clone sacrifices itself to save millions. Luthor murders his research staff at S.T.A.R Labs and founds LuthorCorp, dedicating his life to destroying Superman.
By 1978, the United States is on the verge of social collapse whereas the prosperous Soviet Union has peacefully expanded its influence to nearly every corner of the globe. The cost of this progress is an increased infringement on individual liberties, with Superman fast becoming a Big Brother-like figure; a brain surgery technique that turns dissidents into obedient drones, or “Superman Robots”, is in use. Superman now works with Wonder Woman to save lives as well as govern the Soviet state. Wonder Woman has become enamored of Superman, but he considers her simply as a comrade, and is oblivious to her love for him.
Luthor plans to shrink Moscow, but this plan fails when Brainiac, his collaborator, shrinks Stalingrad instead. Superman intervenes and retrieves both Brainiac's central processing unit and the tiny city, putting an end to the Brainiac-Luthor cooperation. He is unable to restore Stalingrad and its inhabitants to their proper size. This becomes his one failure and a source of great guilt.
Luthor's second plan involves Batman, who is revealed as the boy orphaned by Pyotr. Batman joins forces with LuthorCorp and Pyotr, now head of the KGB. They capture Wonder Woman and use her as bait for Superman, hoping to sap his powers with rays that imitate the light of Superman's native sun. The plan works, but Wonder Woman breaks free and rescues Superman, seriously injuring herself. Rather than face capture and likely lobotomization, Batman commits suicide, and Pyotr is turned into a Superman Robot.
Luthor enacts his third plan when he finds a mysterious green lantern found in an alien ship that crashed at Roswell, New Mexico. Brainiac is reprogrammed into Superman's aide, and the construction of a Fortress of Solitude, located in Siberia and referred to as “The Winter Palace”, begins. Superman's reign continues with no crime, poverty, or unemployment, but with an ever-present state authority. Superman is committed to “winning the argument” with the U.S., and repeatedly refuses Brainiac's suggestions of an invasion. Stalingrad remains his one failure, now contained within a protective glass “bottle”.
Luthor is elected President of the United States, with Olsen as his Vice President. Using his scientific expertise, massive economic capital and dictatorial powers, Luthor returns prosperity to his country. This is only a part of a more general plan to provoke Superman into invading the United States. Luthor shows Olsen two of his greatest discoveries: the Phantom Zone, a place that super-hearing cannot reach; and the Green Lantern Corps.
Luthor confronts Superman in the Winter Palace. Brainiac yanks Luthor deep into the recesses of the Fortress to be converted surgically into a Superman Robot, claiming that Lex would convince Superman to commit suicide in less than fourteen minutes. Superman agrees that his hand has been forced, and prepares to attack.
First Lady Lois Luthor visits Themyscira to forge an alliance with the Amazon empire, now ruled by an embittered and vengeful Wonder Woman. Superman attacks the East Coast, confronting and defeating the Green Lantern Marine Corps, which is led by Colonel Hal Jordan. The Amazon forces, commanded by Wonder Woman, attack Superman but are quickly defeated, along with a collection of “super-menaces” (including Atomic Skull, Parasite and Doomsday) that Luthor has put together over the years. Brainiac's spaceship cuts the U.S. Pacific fleet to pieces, and the two superbeings meet at the White House. They are greeted by Lois Luthor with the last weapon, a small note written by Lex that reads, “Why don't you just put the whole world in a bottle, Superman?”
Realizing he has meddled in affairs that he had no place in, Superman orders Brainiac to end the invasion. Brainiac, however, reveals it has never been under Superman's control, and instead attacks Superman with green radiation (analogous to green kryptonite). Braniac is shut down from inside by Luthor, who evaded surgery. As the singularities powering Brainiac's ship threaten to collapse, Superman rockets it into space, where it explodes. The Earth is saved, but Superman is thought dead.
The Soviet Union falls into chaos, but is soon brought back under control thanks to the Batmen (resistance members who began wearing the costume after Batman's death). Lex Luthor integrates many of Superman's and Braniac's ideas into the new philosophy of “Luthorism” and forms a “Global United States”. This becomes the defining moment for mankind's future as it enters an unprecedented age of peace and stability. A benevolent world government is formed and maintained. Luthor presides over a string of scientific achievements, including the curing of all known disease, and colonization of the solar system. Luthor lives for nearly two thousand years.
At Luthor's funeral, it is revealed that Superman survived the explosion of Brainiac's ship and is apparently immortal. Superman attends the funeral wearing a business suit and thick glasses essentially identical to the appearance of Clark Kent, an identity he never adopted in the Red Son storyline. Luthor's widow, Lois, sees “Clark” in the crowd and, other than an eerie sense of deja vu, suspects nothing. Superman walks quietly away from the ceremony, planning to live among humans rather than ruling over them.
Billions of years in the future, it is revealed that Earth is being torn apart by tidal stresses from the sun, which has become a red giant. Luthor's distant descendant, Jor-L, sends his infant son, Kal-L, rocketing back into the past. The final panels of the comic book depict the landing of Kal-L's timeship in a Ukrainian collective in 1938, effectively causing a predestination paradox.
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