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's Lois Lane,
Earth-Three's
Alexander Luthor Jr., and
Superboy-Prime escape from the
pocket universe to which they had initially fled 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 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 and tries to use his
kryptonite ring. This fails as the kryptonite is not native to Kal-L's universe, and Superman destroys it with his heat-vision. Afterward, Batman 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 attuned to former universes, Alex restores Earth-Two, unpopulated except for the Earth-Two heroes transported there. Superboy-Prime attacks
Conner Kent, this world's Superboy. Multiple super-teams intervene. Superboy-Prime kills
Teen Titans members
Pantha,
Baby Wildebeest, and
Bushido and maims
Risk, ripping off his right arm. The
Flashes and
Kid Flash (Bart Allen) force Prime into the
Speed Force, assisted by the 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. When Earth-Two Lois dies of old age, an aggrieved Kal-L and the younger post-Crisis 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 geared to hunt down and exterminate supers. Alexander selects and merges alternate Earths, trying to create a "perfect" Earth, 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-El what happened to Lois. The answer causes her to break down prompting her to ask Kal-L why. He answers her simply, telling her it was because he chose the wrong Superboy to condemn and the wrong Superboy to condone. When a horde of supervillains attack Metropolis, heroes, current and retired, fly off to the rescue, and 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 in a big bang event, and recreate it with himself as the only superhero. Superboy-Prime is slowed down by a 300-mile thick wall of willpower created by the
Green Lantern Corps, but he kills thirty-two Green Lanterns before Kal-L and Kal-El carry him toward a kryptonite field surrounding the remnants of
Krypton. The Supermen fly Superboy through Krypton's red sun Rao, destroying his armor and causing all three Kryptonians' powers to diminish. Falling to the sentient planet (and Green Lantern Corps member)
Mogo, they fight. Kal-El finally knocks Superboy-Prime out before succumbing to kryptonite poisoning, and the older Superman Kal-L dies of his injuries. Back on Earth, Batman, struggling with Superboy's death and Nightwing's severe injuries sustained during the Metropolis battle, contemplates shooting Alex. Batman is dissuaded by Wonder Woman. Alex manages to escape.
Wonder Woman, Batman, and
Superman later meet up in
Gotham City. 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
Dick Grayson, now healthier, and with
Tim Drake joining him. Superman retires from super heroics until his powers return, focusing his career as a journalist in the meantime. Hiding in an alley in
Gotham City and making new plans, Alexander Luthor is found by
Lex Luthor and the
Joker. The Joker mutilates Alexander by spraying acid onto his face, then electrifies it, and kills Alexander by shooting him as Lex mocks him. The Green Lantern Corps imprison Superboy-Prime inside a red
Sun-Eater. The series ends with him carving an
S into his chest and declaring that he has escaped from worse prisons than this. ==Collected editions==