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 Tatsu 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.
Magpie escapes from Blackgate when she realizes that Batman has a new female partner. Furious, the villainess plans to eliminate her rival and bring Batman to her side once and for all.
Ra's al Ghul and Lady Shiva use the mind-controlled Jason Burr to steal the Ion Cortex. Meanwhile, Tatsu learns the truth about Alfred's connection to her dead father.
Batman is forced to ally with Silver Monkey to escape captivity and stop R'as Al Ghul from conquering Gotham. Meanwhile, Katana and Alfred launch a rescue mission but when they're captured, Ra's reveals Alfred's role in the death of Katana's father.
Ra's Al Ghul releases Batman's enemies from Blackgate Prison, promising them power in return for bringing him the vigilante's head. Meanwhile, Katana is given the choice to kill Alfred and free her father's soul, or let the former MI6 agent go free despite his sins.
The criminal Anarky sets out to frame Batman as a villain, discrediting him with glory-seeking district attorney Harvey Dent.
A mysterious "Golem" protects the residents of Old Gotham from attack by armored figures, and Batman soon deduces that it is Rex Mason, the transformed security guard who became a mutagenic freak.
Humpty Dumpty captures Batman, Katana, Gordon, Mayor Grange and Tobias Whale, and puts them into an elaborate murder mystery. To escape, they must figure out which one of them is guilty of a crime... before it's too late for all of them.
When the Key steals a priceless piece of encryption software only to get arrested, Batman must turn himself over to Harvey Dent so that he'll be locked up and can get the Key out and into Federal custody. However, the head prisoner, Killer Croc, plans to make sure that Batman doesn't leave Blackgate alive.
Bruce is troubled by nightmarish of a twisted man-like bat... and then encounters Man Bat, a mutated scientist who is a pawn in a new scheme by Pyg and Toad. Meanwhile, Harvey seeks Bruce's financial support in his campaign for mayor.
A mysterious Council launches a wave of masked attackers to abduct Ava Kirk, a childhood friend of Bruce's whose father died 20 years ago. Bruce soon discovers that Ava's father, Paul Kirk, is still alive... and has been used as the basis for a clone army.
Anarky hires a mercenary, Deathstroke, on Harvey's behalf to discredit Batman. However, they all discover that Deathstroke will do anything to complete his mission... even turn on his employers. Meanwhile, Bruce and Ava continue to socialize.
Killer Croc lures Batman and Katana into a deathtrap, and only Barbara can save them. However, she's on a date with a boy from school, and Gordon has two detectives trailing her.
"Batman" assassinates Bruce at one of Harvey's campaign speeches, and Alfred and Tatsu set out to find their friend while determining who the imposter is.
Alfred reveals where he was in the months that he was away from Gotham, and Batman realizes that Deathstroke has engineered everything to become Alfred's protege. Meanwhile, an injured Harvey vows to eliminate Batman no matter what it takes.
Deathstroke finds the Batcave and takes Alfred hostage, and Batman must rely on a group of outsiders to defeat out the villain and save his friend. Meanwhile, Anarky and Harvey come to a parting of the ways.