Three years from when Batman died in the eyes of the world, killed by Superman, the media is crying out for its lost heroes. Batman sends Caroline Keene Kelly, his new sidekick, to collect Professor Ray Palmer, the Atom. After regrouping at the Batcave, the Atom, Kelly and some of Batman's men storm a complex and free the imprisoned Barry Allen, The Flash. Superman destroys a giant asteroid that was streaking on a collision course with Earth. He then meets with Wonder Woman. She meets with Superman and Captain Marvel. The three are being blackmailed by Lex Luthor and Braniac into doing their bidding. Luthor orders the three heroes to find out who is responsible for the freedom of the Flash and the Atom and to bring that person or persons to them. Superman flies to see Batman and fights a giant dinosaur robot and a Bizarro robot. Next, the Flash puts several explosive devices on Superman and explodes them, causing 90 tons of rock to fall on Superman. Then Green Arrow shoots a Kryptonite arrow at Superman, weakening him enough for the Atom to shrink down and jump into Superman's ear, throwing off his equilibrium. Then Batman appears wearing Kryptonite gauntlets, pummels Superman and tells him to get out of his cave.

The most eagerly-awaited sequel in comics begins! Three years after the events in THE DARK KNIGHT RETURNS, Batman knows the world is nowhere near the perfect little place it pretends to be, and he sees the cracks in the system that have been neatly covered up. It's time to find where all the heroes have gone, and the Dark Knight is the right man for the job.