Two villains, Professor Pyg and Mr. Toad, swear revenge on three Gotham millionaires... and one of them is Bruce Wayne. Meanwhile, Bruce tries to cope with an overprotective Alfred, who takes measures to make sure that his ward is safe.
A new villain arrives in Gotham: Magpie, a woman with razor-sharp claws and an uncanny healing ability. She is hunting down psychiatrists and Batman has to find out who Magpie is and what she wants if he hopes to stop her. Meanwhile, Bruce begins testing Tatsu.
While Bruce tries to determine if Tatsu can function as his bodyguard, a new villain named Anarky goes on a rampage across Gotham.
The League of Assassins come after a Wayne Industries scientist and Katsu is forced to guard him at the manor... and face an enemy from her past.
A new criminal genius captures criminals and imprisons them in life-size toy soldiers... rigged to explode. Batman soon discovers that the villain is seeking revenge on the people he holds responsible for his plight.
When a security guard is transformed into a monstrous freak by an industrial accident, Batman becomes involved when the guard, Rex Mason, goes on a rampage.
After discovering that Alfred and Tatsu have betrayed his trust, Bruce turns to Bethany... who is secretly working with the League of Assassins in an attempt to regain the Soultaker Sword.
Tobias Whale has one of his underlings abduct Barbara Gordon as leverage against her father, and Lt. Gordon turns to Batman for help. Meanwhile, Batman finds himself working with a new partner whose style clashes with his own.
Cypher, a villain with the ability to control others, goes after Jason Burr in an attempt to gain the Ion Cortex for the League of Assassins.
Anarky launches a new plan, convincing Lady Shiva to break into a CRC facility in return for his giving her back a crate containing a treasure belonging to the League of Assassins.
Pyg and Toad are back, committing eco-terrorism against fashion designers and models. But Batman soon realizes that their crimes are only diversions from their true goal.