Plot
On an alternate Earth, Joker and Harley Quinn kill Jimmy Olsen, kidnap a recently pregnant Lois Lane, and steal a nuclear weapon, which they connect to a heart rate monitor linked to Lois's heart. Upon hearing of Lois's capture, Batman calls the Justice League to find her. The Flash finds the Scarecrow dead in his lab and his supply of fear toxin missing before being killed by a trap laid by Joker.
Lois's husband, a panicking Superman, eventually finds Joker and Harley hiding on a submarine but is attacked by Doomsday, whom he punches into space. As the other heroes arrive and apprehend the Joker and Harley, Batman realizes that they have mixed the fear toxin with Kryptonite and used it to make Superman hallucinate that he is fighting Doomsday; in reality, he has beaten Lois to death. When her heart stops, the bomb attached to her detonates, destroying Metropolis and killing 11 million people. Joker reveals to Batman that he was tired of losing to him, so he decided to target Superman and the Flash instead. Suddenly, a grief-stricken Superman then kills Joker in revenge.
While Green Arrow takes Harley to his hideout to protect her from Superman, the latter reveals his identity before the United Nations and announces his intentions to bring peace to Earth, by force if necessary. The Justice League is left divided over Superman's actions; some members, such as Wonder Woman, support his new methods, while others, like Batman, keep their no-killing vow. Other heroes, such as Aquaman, Shazam, and the other magic users, refuse to choose sides and leave the League. Hal Jordan also leaves, stating that he and his fellow Green Lanterns are being recalled to Oa.
Meanwhile, the United States government becomes concerned that Superman will interfere in their operations, and have Mirror Master kidnap Jonathan Kent as leverage against him. Superman begins to question his actions, but Wonder Woman reassures him that he is doing the right thing and offers to help him find Jonathan. Confronting Mirror Master, Wonder Woman learns Jonathan's whereabouts, allowing Superman to rescue him. Elsewhere, Batman confronts the President and warns him that Superman will kill him if he finds out that he ordered Jonathan's capture.
Later, Superman visits Batman in the Batcave to make peace, but they get into an argument over their ideological views, and Batman refuses to join Superman. While trying to stop Superman from relocating Arkham Asylum inmates to a more secure facility, Batman and Nightwing are shocked to discover that Robin has joined Superman. Harley, who escaped Green Arrow's capture and decided to become a hero, releases the inmates, forcing Batman and Superman to temporarily put their differences aside to fight them. During the battle, Robin lashes out in anger and unintentionally kills Nightwing, leading to Batman disowning him. In the afterlife, Nightwing meets Rama Kushna, who transforms him into Deadwing.
Robin attempts to convince Superman to ally with Ra's al Ghul, but the latter declines. Batman forms an underground resistance and plans to steal a red sun cannon from the Fortress of Solitude. During the break-in, Superman overpowers Captain Atom, Ra's kills the Atom and destroys the cannon, and one of Green Arrow's shots is casually deflected by Superman, accidentally killing Jonathan, whom Superman had been keeping safe at the Fortress, causing Superman to murder him in response. After Superman transforms the Earth into a police state using surveillance drones, Batman has Plastic Man break Mister Terrific out of prison and leaks video footage of Superman killing a group of partying teenagers inspired by Joker to ruin his public image, shocking Wonder Woman as a result.
In response, Superman allies with Ra's and dispatches Amazo to enforce global peace. However, the android quickly turns violent in Smallville as Ra's had secretly programmed it to kill Superman. Amazo kills Hawkman and Cyborg, but Batman and his allies arrive and help Superman and Wonder Woman destroy the android. Meanwhile, Robin, having had a change of heart, defeats Ra's with Deadwing's help in a duel, sparing Ra's life.
Despite their aid, Superman prepares to have the Insurgents arrested and incapacitates Wonder Woman after she turns on him, but is confronted by a Superman from an alternate Earth, whom Mr. Terrific had summoned. Mr. Terrific claims the other Superman is from Earth-9 and their world is Earth-1, but the other Superman corrects him, saying that his Earth is Earth-1 and the Injustice universe is Earth-22. Injustice Superman defeats his counterpart as the latter was holding back, but surrenders after being met with a Lois from another alternate Earth who lost her Superman after becoming pregnant with his child. Lois reminds Injustice Superman that, just like for hers, all life is sacred. Realizing how far he has fallen, Superman willingly agrees to be imprisoned.
Although unsure of what will happen next, Batman makes preparations to rebuild the world and his life with Catwoman.
