Story SummaryChapter 1: The first chapter opens in the time period of the game, as Batman reflects on Superman's tyrannical regime. From there, the story flashes back five years previous. Superman (who is married to Lois Lane in this version of the DC Universe), learns that Lois is pregnant and reacts with a mixture of excitement and fear. However, a news tip leads Lois and Jimmy Olsen to the Metropolis docks, where they're ambushed by Joker and Harley Quinn. Joker immediately shoots and kills Jimmy.
Chapter 2: While Batman investigates a theft at STAR Labs, Superman discovers Jimmy's body and the bloody playing card Joker left at the scene. Superman fratically pleads for Batman's help, who calls in the entire Justice League to assist in the search. Flash leads Batman to Scarecrow's secret laboratory, where they find that the villain has been poisoned by Joker's toxin. Wonder Woman learns from a dock worker that Joker and Harley are hiding in a submarine. Superman confronts the duo, but is dosed with a toxic gas and is attacked by what looks to be Doomsday.
Chapter 3: Superman immediately begins battling Doomsday and carries him into space. Joker and Harley attempt to flee their submarine (which Harley named Gunter), but are apprehended by the Justice League. Batman discovers that Joker stole Scarecrow's fear toxin, laced it with Kryptonite, and used it to infect Superman. Joker also reveals that he hid a nuclear warhead in the center of Metropolis, programming it to detonate once Lois' heartbeat stops. In orbit, Superman realizes too late he had been brainwashed into attacking his wife, not Doomsday. As Lois and her unborn child both die in the vacuum of space, the warhead detonates and destroys Metropolis.
Chapter 4: Superman mourns Lois' death amid the ruins of Metropolis while the Justice League rescue survivors from outlying areas. Meanwhile, Batman interrogates Joker in a Gotham City prison. Joker reveals that he targeted Superman because he was tired of losing to Batman and wanted "to play on Easy Mode for a while." Despite Green Lantern's efforts to stop him, Superman flies to the prison and punches Joker through the chest while the villain dies laughing.
Chapter 5: Harley Quinn escapes police custody and returns to Joker's secret hideout, mourning the death of her "puddin'." Green Arrow quickly tracks her down and takes her into custody, hoping to prevent her from being Superman's next murder victim (as much for Superman's own sake as for Harley's). He drives her to his Arrow Cave, which is impervious to Superman's X-ray vision. Harley admits that she knew Joker was an evil man but couldn't help loving him anyway. Before departing, Green Arrow cheers Harley up by giving her his best maniacal laugh.
Chapter 6: Superman continues to mourn the loss of his family and city in the Fortress of Solitude. News broadcasts of a civil war in the Middle Eastern country of Bialya compel him to intervene. Superman rescues a group of civilians and kidnaps the Bialyian president. Wonder Woman convinces him to clean himself up and give a speech to the United Nations. The following day, Superman announced his former civilian identity to the world and delivers an ultimatum - all world governments must cease hostilities, or Superman will do it for them.
Chapter 7: Superman continues his worldwide crusade, stopping a US drone attack in the process. A military leader convinces the President that steps need to be taken to reign in Superman. A small squad led by the supervillain Mirror Master is sent to kidnap Superman's adoptive parents. Mirror Master burns their house down and traps the Kents inside a mirror. He orders Superman to stand down immediately or risk his parents being tortured and killed.
Chapter 8: Wonder Woman assembles the Justice League to inform them of the Kents' kidnapping and reaffirm her belief in the righteousness of Superman's quest. The League members team up to hunt down each of Flash's Rogues until Mirror Master is finally tracked down at World's End Bar in Keystone City. Mirror Master admits to hiding the Kents in the vast salt flats of Bolivia. As Superman rescues his parents, Batman confronts the President and admonishes him for targeting innocents and giving the Justice League a reason to rally around the fallen hero. The President questions whether Superman can be trusted any longer, knowing as he does about the corruptive influence of absolute power.
Chapter 9: Wonder Woman carries on Superman's crusade as she stops a war between Qurac and Justal. Greek god of war Ares confronts her about Superman's actions. Wonder Woman calls Superman "the greatest man I've ever known" and admits her desire to become his lover after his grieving process is done. She realizes Ares is frightened at the prospect of Superman and herself having children. Though Ares attacks her, Superman arrives to aid her and Wonder Woman brutally stabs Ares. She leaves the god of war to languish in the desert, hoping that an enforced peace will cause his powers to fade. Ares reflects that Wonder Woman may be Superman's final undoing, as she lacks his restraint in battle.
Chapter 10: Superman enters the Batcave as Robin and Nightwing are sparring. He confronts Batman about his disappearance during the manhunt for the Kents and insists that he's only doing what Batman would do if he had the powers of a Kryptonian. Batman in turn chides Superman for resorting to murder, warning that once a horrible action is justified once, it becomes easier to justify again. Meanwhile, Aquaman and his Atlantean army attack a Japanese whaling fleet. The Justice League attempt to rescue the whaling crew and are drawn into a conflict with the Atlanteans.
Chapter 11: The war between the Justice League and Atlantis rages on as Batman and Superman continue to argue in the Batcave. Superman argues that Batman loved having Joker as a nemesis, despite the casualties their rivalry caused. Batman lashes out and punches Superman, merely breaking his hand as a result. Batman then admits that Superman has always been the better man, but refuses to join him in his crusade. Aquaman calls forth an Atlantean superweapon, causing a tsunami wave to emerge and engulf the shipping fleet. The source of the tsunami is revealed to be a Kraken.
Chapter 12: Superman emerges from the Batcave to join the fight against Aquaman. Batman radios Aquaman to warn him of Superman's unhinged mental state. While Aquaman initially agrees to back down, the Justice League realize he was only bluffing while his armies invaded several major cities worldwide. In retaliation, Superman raises Atlantis from the ocean floor and deposits it in the middle of the Sahara Desert. Aquaman finally relents, while heroes like Green Lantern and Shazam begin showing doubts about Superman's actions. Superman revokes Batman's access to the Justice League communicators, while Wonder Woman reassures him their actions were just. However, she pointedly neglects to pass along Aquaman's condolences about Lois' death.
Chapter 13: The Justice League find themselves quelling an anti-superhero riot in Melbourne, Australia. A local hero named Galaxor attempts to drive the League away, but is brutally injured by Superman and Wonder Woman as Flash looks on. Distraught, Flash flees the scene and is directed by Batman to the laboratory where Galaxor lived and worked. Realizing the young hero had idolized the Justice League, Flash's faith in Superman is further fractured. He runs through the Australian wilderness, trying to ignore his growing inner turmoil.