The story of how the Commissioner's daughter became Batgirl and how her best friend becomes Poision Ivy is told.
Continuing where we left off in the first part, Barbara Gordon becomes Batgirl in order to save the commissioner, but does Batman really want a sidekick?
Bruce Wayne suffers amnesia when fighting against Penguin, forgetting his role as Batman, and leaving him able to continue his crime spree. Barbara, who suspects he is Batman but later believes she is mistaken, tries to stop Penguin but is soon captured. With Batgirl in trouble, Alfred decides it's essential for Bruce to relearn his role as Batman if she is to stand any chance of rescue.
After he is captured once again, Arnold Wesker is released from Arkham when Dr. Hugo Strange "cures" him by removing Scarface from him, allowing the former criminal to use his ventriloquism to start a new career as a children's entertainer. Batman is initially suspicious of this, but gives Arnold the benefit of the doubt, unaware that Strange plans to reunite him with his former puppet, which soon brings trouble.
While partaking in a charity race, Bruce witnesses Gearhead, a villain who can take over anything mechanical and transform it with nanomachines into a powerfully fast vehicle, to steal the race's prize. Both Batman and Batgirl attempt to stop him, but when Gearhead destroys the Batmobile, Bruce decides to build a better one that can bring down the villain.
Batman and Batgirl find themselves dealing with new trouble from Joker, when he manages to get a hold of Bane's Venom Infusion system to become a true comedy "powerhouse". With his new-found strength, Joker's latest crime spree seems unstoppable, especially when Batgirl accidentally causes Batman to be captured when she borrows his power suit. To rescue him, Batgirl discovers that she must overcome her own limitations to master control of the suit as well as stop Joker.
Catwoman seems to be the suspect in the theft of a rare Black Siberian Leopard, but it soon turns out that Joker is behind the theft when Batman and Batgirl investigate and attempt to protect a second leopard of the same breed, unaware that Catwoman is interested in the matter. When all three discover that the cats were stolen for Killgore Steed, the owner of several dangerous creatures, no one anticipates Joker double-crossing him and using his personal maze and creatures to put an end to Batma
When Gotham's police and government officials, including Mayor Grange and Commissioner Gordon, enact strange, new laws, Barbara discovers that the cause is a mysterious plant that they all received. Batman and Batgirl soon discover that Poison Ivy is responsible and that she has replaced the officials with plant-based copies, leading the pair to stop her and her clones, while finding where the real officials have been taken to.
Cosmo Krank seemed to be an ingenious toymaker, but all of his creations were dangerous for kids to use, leading to Bruce and Wayne Industries shutting his company down. Bruce soon finds himself as the target of the toymaker, who seeks revenge by killing him with newer, diabolical versions of his toys. Knowing that Batman must bring him down, things are not so easy when Commissioner Gordon assigns Detective Cash to be Bruce's bodyguard until the demented villain is arrested, forcing Bruce to fin
Upset that Batman and his new sidekick, Batgirl, are ruining his plans, Joker decides that he needs a partner of his own. He soon finds the right person in Donnie, a misguided prankster who attends classes at the same high school as Barbara. When she realises that Donnie is Joker's new sidekick called Prank, she and Batman find themselves trying to convince him that Joker is not a good role model to have.
No one could have anticipated that Maximillian Zeus, a technology entrepreneur, billionaire, and Greek and Roman history fanatic, would seek to take control of Gotham, but it does when he looks set to lose to Mayor Grange during a mayoral election. Using a giant aircraft called New Olympus that is equipped with a powerful weapon and crewed by his personal security force of "Gladiators", he soon threatens the city leaving Batman to stop him. But he soon discovers that Batgirl is far more resource
Alfred is surprised when an old school friend of his turns up in Gotham and invites his friend on a treasure hunt. Although weary of his friend, Alfred agrees, unaware that the treasure being sought out for, is the target of both Penguin and Mr. Freeze. Batman is forced to join the hunt, and soon deduces that the treasure lies beneath Gotham Bay.
A new villain emerges in the form of D.A.V.E. (Digitally Advanced Villain Emulator), an AI database created by Hugo Strange that is encoded with the minds of Gotham's greatest criminals and breaks free to commit crimes. Batman finds himself trying to stop D.A.V.E., when the AI proclaims itself as the ultimate criminal and plans to reveal to Gotham the true identity of Batman, unaware that things are not what they seem to be.