The Joker steals an atomic bomb, and it is up to Batman and Robin to find and stop him. Since there is no time to spare, the duo enlist the help of Harley Quinn to track Joker down. 

Gotham's new DA, Janet Van Dorn, is out to capture Batman, but both she and him end up captured by a gang of criminals instead. They are soon put on a kangaroo trial by the Joker (the judge), Two-Face (the prosecutor), the Ventriloquist (the bailiff), Poison Ivy, Harley Quinn, the Mad Hatter, Killer Croc, the Scarecrow, the Riddler, and other criminals. If the defense (Batman and the D.A.) can prove that Batman is not the cause for everyone's turn to crime, they will be set free. When the jury gives the verdict of 'not guilty', the villains have little intention of following through on their deal.

A mystic Egyptian scroll donated to the Gotham museum by Bruce Wayne is stolen by Ra's al Ghul, and Batman and Talia must join forces to prevent the power-mad Ra's from unlocking the scroll's secrets of life and death. Their quest takes them to a hidden temple deep beneath the Egyptian desert. There, the Dark Knight is forced into a terrifying battle with an ancient Egyptian sorceress.

En route to an upstate prison, Killer Croc escapes and leads Batman on a dangerous chase through the wilderness. After throwing Batman temporarily off his trail, the reptile-man takes refuge with a group of retired circus freaks, and convinces them to help him. When Batman arrives, Croc and the freaks band together to capture him.

Not only has Poison Ivy been released from Arkham Asylum, but she's also married to her doctor and settled down to help him raise his two sons. It would appear that Ivy has gone straight and that her old days as a criminal are over. But wealthy bachelors are being struck down by an unknown toxin, leaving Batman to question Ivy's innocence.

Dr. Matthew Thorne, losing his medical license and forced into becoming the crime doctor by his younger brother, crime boss Rupert Thorne, must perform delicate surgery on Rupert. He can't do it alone, and kidnaps Dr. Leslie Thompkins to assist. Batman discovers Leslie's disappearance, and rushes to track her down - and has an additional interest in Matthew, because he was a medical school classmate of Bruce Wayne's father Thomas.

Wealthy socialite Veronica Vreeland returns from Central America, bringing tiny handmade dolls for all her friends. According to native legend, once placed under a pillow, the dolls do the sleeper's worrying for them. Unknown to Veronica or her guests, each of the dolls was made by the Mad Hatter, and contains a tiny microchip which plants hypnotic suggestions inside the sleepers' brains.

Clayface is falling apart, literally. His clay-like body is disintegrating. Fortunately, a scientist he knew from his movie star days is working on a remedy. However, Hagen is forced to steal money to pay for the expensive components of the remedy. That is, until one of his targets is Wayne Biomedical Labs...

Robin discovers that Gil Mason is in league with the underworld and goes to investigate him. He encounters Batgirl along the way, and go their separate ways to stop Mason. They then meet again to learn that Gil is working with Two-Face to take out Gordon, and have Batman (as Matches Malone) captured.

When Commissioner Gordon is framed for taking bribes from Rupert Thorne, his daughter Barbara pleads with Batman to show up at a rally being put on in the commissioner's behalf. But when Batman disappears after finding the person behind the frame-up, Barbara takes the law into her own hands as Batgirl.