After the Joker destroys Metropolis and tricks Superman into killing Lois Lane and their unborn child by making him believe he is fighting Doomsday (Lois's death setting off a nuclear bomb that the Joker had linked to her heartbeat), Superman murders the Joker in front of Batman in a fit of rage and establishes a new world order. A battle ensues between the forces of Superman's Regime and those allied with Batman's Insurgency. The Insurgency discovers an alternate universe where the Joker's plan did not succeed and transport several of its super heroes to theirs in order to help them defeat the Regime.
Having arrived in this world, attempting to learn what has happened, Aquaman travels to Atlantis to research the archives while Green Lantern goes to recharge his ring. After defeating Raven and Cyborg in battle when he discovers them torturing Deathstroke, Green Lantern faces Sinestro and his own counterpart as they attempt to capture Wonder Woman and Green Arrow, subsequently meeting the Batman of this world. Learning that Atlantis has agreed to a treaty that puts Superman in near-total control of Atlantis' army, Aquaman rejects the treaty, defeating the Flash, Shazam and his own counterpart before Ares appears. Acknowledging that he is weakened by the lack of conflict, Ares sends Aquaman to join the Insurgents, which includes a Lex Luthor who was never a criminal. Batman explains that he has a weapon that can defeat Superman in the Batcave, but it requires DNA samples from the other four heroes to unlock as Batman wanted to ensure he could not make the decision to stop Superman by himself (The heroes being required as Green Arrow is dead and the other three are allied with Superman).
Transported to this world along with the heroes, the Joker defeats 'his' Batman in time for the Regime to capture him, only to subsequently ally himself with the Harley Quinn of this world. After Harley's gang are attacked by Nightwing and Hawkgirl, they are rescued by the heroes, who travel to the Batcave to recover the weapon. Meanwhile, the heroes of the other world attempt to recover their comrades, but their first attempt merely sends Cyborg to the darker reality. Cyborg overhears Lex Luthor and Deathstroke discussing plans to defeat Superman, prompting a brief clash before the other displaced heroes explain the situation to him.
With Cyborg and Deathstroke having taken control of the teleportation system on the Watchtower, the heroes stage a break-in to rescue the displaced Batman from his planned execution, but Luthor's attempt to use the kryptonite weapon against Superman fails, resulting in his death. Overhearing humanity's fear of him, Superman decides to destroy Gotham City and Metropolis to demonstrate the chaos that would arise in his absence, but when he kills Shazam for questioning him, the Flash realizes that the heroes have gone too far and defects to the Insurgents. With the kryptonite weapon useless, the dimensionally-displaced heroes suggest recruiting the Superman of their world to stop this one, only to be interrupted by a villain attack.
During the fight, Wonder Woman is contacted by Ares, who reveals that Superman's plan will be carried out by an army of Amazons, Ares wanting to stop this plan as Superman's victory will mean an end to the conflict that empowers him. Accepting his advice, Wonder Woman defeats Raven and her other self before convincing the Amazons to return to their former role as protectors rather than conquerors. As the battle begins, Batman convinces his counterpart to have faith in their Superman just as he had faith in the other displaced heroes. Superman arrives in this world in time to defeat Black Adam and Aquaman while Wonder Woman's Amazon army holds back the armies of Atlantis.
After defeating Doomsday in the Fortress of Solitude and trapping him in the Phantom Zone, Superman faces his counterpart, rejecting his other self's attempt to defend his actions as enforcing authority over an unworthy humanity and informing him that Lois would be disgusted at what he has become. With the other Superman's defeat, the rest of the Regime are either rounded up or turn themselves in, and the other Superman is placed in a prison where he is exposed to red sun radiation, negating his powers. As he talks with the other Batman about the new transitional government being established, the displaced Superman acknowledges that he could have become his counterpart, but Batman merely grimly notes that he hopes Superman never has to learn what he could be capable of while vowing to be there if Superman ever falls that far.
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