As a battle rages in the seas between the heroes of Atlantis and their enemies, the Spectre emerges in destructive fury against both friend and foe. The battle between the Amazons on Paradise Island and the OMACs does not go well as their forces are totally overwhelmed, with Wonder Woman making the hard choice that the Amazons must leave this realm of existence by the protection of the gods. The gathered heroes at New Cronus arrive at the center of the universe where they deal with a powerful maelstrom as well as the warring Thanagarian and Rannian ships in that vicinity. Superman comes to the help of the Shadowpact in El Paso, Texas while Jaime Reyes finds the Blue Beetle Scarab. Wally West rushes off as the Flash to deal with a super-tornado in Kansas City.
Batman is frustrated at his inability to stop Brother Eye from carrying out Program Truth And Justice when Earth-Two Superman visits him, telling Batman that the Dark Knight he knew on Earth-Two was a man that lived past the death of his parents, allowing himself to love, to marry, and have a child. Kal-L tries to reason with Batman that the best course of action is to allow his own reality to be replaced with that of Earth-Two, which he believed held more promise than the one Batman knew. Unfortunately, Batman questioned whether that reality's Dick Grayson was a better version of his own's, and so attempted to use Lex Luthor's Kryptonite Ring on Kal-L to no effect, only for Kal-L to burn it off Batman's finger with his heat vision.
Lex Luthor discovers his doppelganger's hideout and confronts him, only to be overpowered by both his opponent's intellect and his power. Fortunately, Lex Luthor manages to destroy a computer in the hideout, exposing the doppleganger as Alexander Luthor using a holographic projection over himself. Then Superboy-Prime sneaks up from behind and rips Lex Luthor's battlesuit off him, then is ordered by Alexander Luthor to dispose of him. However, Lex Luthor teleports himself away before Superboy's heat vision touches him.
Power Girl takes some time away from visiting Lois Lane-Kent to think of whether she would be willing to help restore the reality that Kal-L and his wife once knew and reenters the hideout with her answer when she notices a giant machine with part of the Anti-Monitor's corpse attached to it. She notices that several superheroes are also attached to the machine, unconscious, which included the Martian Manhunter, who was last seen at the JLA Watchtower on the moon. Power Girl flies up to where J'onn J'onnz is located and asks if he is okay when she is attacked from behind. It is Superboy-Prime and Alexander Luthor who did this, with Superboy-Prime saying that he knew she would never help them and Alexander saying that she will help them whether she wants to or not.
In the Batcave, Batman plays back what his "black box" has recorded about the intruder posing as Superman who has infiltrated the Watchtower, destroyed it, and made off with Martian Manhunter. The evidence reveals that it was Superboy-Prime who did it.