The story begins in the wake of the four lead-in limited series, with Superman, Wonder Woman, and Batman feuding, the JLA Watchtower destroyed, and the heroes of the world all facing a variety of menaces. Over this backdrop, Kal-L (the Earth-Two Superman), along with Earth-Two Lois Lane, Earth-Three Alexander Luthor, and Superboy-Prime escape from the pocket universe where they had been left at the end of Crisis on Infinite Earths. Kal-L seeks out his cousin, Power Girl, also a survivor of Earth-Two. Believing Lois' health will improve on her native world, he hopes to replace the current Earth-One with Earth-Two, which he considers perfect.

Kal-L tries to enlist Batman's support, stating that the Post-Crisis Earth's inherent "bad" nature caused Batman's recent mistrust and hostility. Batman refuses. Afterward, he learns Superboy-Prime destroyed the JLA Watchtower.

Alexander reveals to Power Girl that he and Superboy-Prime had been leaving their "paradise" for some time, manipulating events to help create an inter-dimensional tuning fork. Using the Anti-Monitor's remains and captured heroes and villains specifically attuned to former universes (Power Girl among them), Alex restores Earth-Two, un-populated except for the Earth-Two heroes transported there.

Superboy-Prime attacks Conner Kent, this world's Superboy. Multiple super-teams intervene. Superboy-Prime accidentally kills several heroes before the Flashes and Kid Flash force him into the Speed Force, assisted by speedsters already within it. Jay Garrick, the only speedster left behind, says the Speed Force is now gone.

Seeking to create a perfect world, Alexander restores many alternate Earths. The Earth-Two Lois dies, and an aggrieved Kal-L and the younger Superman Kal-El fight until Wonder Woman separates them. Bart Allen (wearing Barry Allen's costume and aged to adulthood) emerges from the Speed Force, warning that he and the other speedsters were unable to hold Superboy-Prime, who returns wearing Anti-Monitor inspired armor that stores yellow sun radiation to empower him, making him even stronger.

Batman's strike force destroys Brother Eye, a satellite AI created by Batman that had gone rogue and begun transforming civilians into nano-infused robots. Alexander selects and merges alternate Earths, trying to create a "perfect" world, until Firestorm blocks his efforts. Conner, Nightwing, and Wonder Girl release the Tower's prisoners. Fighting each other, Conner and Superboy-Prime collide with the tower, destroying it. The multiple Earths recombine into a "New Earth" as Conner dies in Wonder Girl's arms. Power Girl soon arrives and asks Kal-L what happened to Lois. The answer causes her to break down prompting her to ask Kal-L why. His answer is because he chose the wrong Superboy.

When a horde of supervillains attack Metropolis, heroes, current and retired, fly off to the rescue. They are joined by the National Guard. The battle results in multiple deaths on both sides, including many by Superboy-Prime himself, who kills villains and heroes alike. During the battle, Superboy-Prime takes off to destroy Oa, planning to collapse the Universe, and recreate it with himself as the only superhero. Superboy-Prime breaks through a 300-mile thick wall of willpower, and then kills thirty-two Green Lanterns before Kal-L and Kal-El carry him toward Krypton's remains, now essentially a huge cloud of kryptonite. Flying through Krypton's red sun Rao destroys Superboy-Prime's armor and causes all three Kryptonians' powers to dissipate. Landing on the sentient planet (and Green Lantern Corps member) Mogo, they fight. Kal-El finally knocks Superboy-Prime out and the older Superman Kal-L dies of his injuries in the arms of his cousin, Power Girl.

Back on Earth, Batman, struggling with Superboy's death and Nightwing's severe injuries sustained during the Metropolis battle, contemplates shooting Alex. Batman is discouraged by Wonder Woman. Alex manages to escape.

Wonder Woman, Batman, and Superman later meet up in Gotham. Wonder Woman plans to find out who she is. Batman plans a similar journey of self-discovery, revisiting the training of his youth, this time with d*** Grayson, now healthier, and Tim Drake joining him. Superman retires from superheroics until his powers return. He is just Clark Kent a reporter and also spending time with his wife Lois Lane and family and reporter on the missing year [See 52 comics to find out]

Hiding in an alley in Gotham City and making new plans, Alexander Luthor is found by Lex Luthor and the Joker. The Joker deforms him by spraying acid onto his face, then kills Alexander as Lex mocks him for making the mistake of not letting the Joker play in the Society.

The Green Lantern Corps imprison Superboy-Prime inside a red Sun-Eater. The series ends with him carving an S into his chest with his bare hands and declaring that he has escaped from worse prisons than this.