Batman works out Deathstroke's plan to discredit him, while a deranged Harvey Dent launches a final assault to capture the Caped Crusader so that he can execute him.
A Batman imposter shoots and seemingly kills Bruce Wayne. While Alfred and Tatsu try to find their friend, Harvey Dent declares a city-wide hunt for Batman since the vigilante has become a murderer.
Barbara tries to balance her personal life and her "career" as Oracle when Killer Croc captures Batman and Katana in a deathrap while she's on a date.
Gotham gets a new hero when Harvey brings in the mercenary Deathstroke as a new member of his SCU. However, it soon becomes clear that Deathstroke has his agenda... and will do whatever it takes to achieve it.
Mysterious figures are stalking a scientist, and Batman soon learns that they are also going after an old friend, Ava Kirk. Ava's dead father, Paul, resurfaces and explains that the figures are his clones... and they will stop at nothing to capture him.
Batman is haunted by a mysterious winged bat-like man, only to discover that he really exists. Meanwhile, Alfred returns and tries to deal with Bruce's personal issues.
Batman has himself arrested in order to abduct a high-tech thief locked up in prison. However, he discovers that the prisoner in charge, Killer Croc, wants the Key for himself.
Batman, Katana, Commissioner Gordon, Mayor Grange, and crime lord Tobias Whale are abducted by Humpty Dumpty and forced to play a macabre game to find out which among them is guilty of a crime. However, none of them know what the crime is or who did it.
Batman and Katana investigate a mysterious "Golem" that is protecting the people of Old Gotham, and discover that it's the transformed Rex Mason, now an elemental freak. Meanwhile, Harvey gets a new partner.
Six months after the blackout, DA Harvey Dent has been elected to put a stop to Batman. Meanwhile, Batman is framed for an attack on Mayor Marion Grange.
Batman races to save the city from Ra's al Ghul, but finds himself opposed by his arch-villains when Ra's releases them from Blackgate Villain to hunt the Caped Crusader down. Meanwhile, Katana must choose whether to kill Alfred and free her father's soul, or let the former agent live.
Batman must team up with fellow prisoner Silver Monkey to escape the League of Assassins. Meanwhile, Ra's al Ghul reveals the truth to Tatsu about Alfred's involvement with her father's death.
Ra's al Ghul uses the mind-controlled Jason Burr to steal the Ion Cortex from Wayne Industries and plunge Gotham City into darkness.
Magpie breaks out of prison and goes on a rampage, determined to kill Batman's new partner Katana and make herself his sidekick.
While Batman trains Katana in how to use her instincts, Professor Pyg and Mr. Toad launch a new series of crimes on behalf of animal kind.
Batman and Katana partner up to investigate a break-in at a CRC facility, and discover that Anarky plans ton unleash a toxin on Gotham City that turns humans into rampaging monsters... and Lady Shiva is willing to help him do it.
Cypher, a part-robot villain with powers of mind control, is seeking the Ion Cortex.
A reluctant Lt. Gordon turns to Batman and his new ally, Katana, when Barbara is kidnapped.
A date with Bethany Ravencroft turns into disaster for Bruce when he discovers that it's a trap to let the League of Assassins recover the Soultaker Sword.
A security guard is exposed to toxins which transforms him into a creature capable of transforming his body into any element.
Batman teams up with a reluctant Lt. Gordon to take on a villain who leaves his victims imprisoned in life-sized toy soldiers rigged to explode.
Katana is forced to protect a Wayne Industries scientist using the Soultaker Sword in her keeping, to stop an enemy from her past.
Bruce must take to the streets to fight a new villain, Anarky, while testing Katana to determine if she is loyal to him.
Magpie, a villainess with multiple personality disorder, abducts Batman and he must work out who he's dealing with to have any hope of defeating her.
While Batman squares off against a pair of vigilantes, Alfred realizes that he's too old to protect Bruce and hires a bodyguard for him... the mysterious Katana.