Eco-terrorists Professor Pyg and Mister Toad are hunting Gotham City's resident billionaires Simon Stagg, Michael Holt and Bruce Wayne to make them pay for their crimes against nature. Now, with the stakes being the billionaires' lives, Batman has to solve this case fast but when Wayne's butler, Alfred, is kidnapped in Bruce's place, Batman must save him. Later, Alfred hires a new bodyguard for Bruce: Tatsu Yamashiro.

Batman is hot on the heels of an extremely dangerous thief named Magpie, who not only sports razor-sharp fingernails laced with poison but is also invulnerable to pain. But Batman is not the only one after her. Lieutenant James Gordon is after her as well, and the two will ultimately go head-to-head to catch her.

A new villain has arrived in Gotham to challenge Batman: Anarky. Resembling a ghost image of Batman, Anarky prides himself on his brilliance and intends to prove it to Batman by manipulating a pair of street thugs, Junkyard Dog and Daedalus (known as Doodlebug in the comics), to do his bidding. But Anarky's real plan is far more devastating: seeking to create a disaster seen by all of Gotham and proving once and for all that even the great Batman is powerless to protect his fair city from the clutches of Anarky.

Introducing the prototype of his newest product to the entire world, the Ion Cortex, a device capable of solving the world's energy crisis, Bruce Wayne hires brilliant scientist Dr. Jason Burr to work on the project. The announcement also draws the attention of the League of Assassins. When Silver Monkey, one of the League's members, attacks Wayne Manor, it is up to Alfred and Katana to keep the assassin at bay until Batman returns. But Katana is armed and ready for the task with the legendary Soultaker Sword, a sacred weapon she stole from the League of Assassins back when she used to work for them.

Ra's al Ghul recruits all of the imprisoned super villains to eliminate Batman in exchange for control of a piece of the city. Ghul makes an offer to Katana: kill Alfred and he will release her father from the Sword of Souls, who has been trapped ever since Alfred escaped from him long ago. Before killing Alfred, Katana wants to hear the truth from him. Alfred tells her that her father sacrificed himself. When Ghul captured the two men year ago, the sword was about to drain Alfred's soul, and her father took his place. This allowed Alfred to escape. With this new information, she refuses to kill him. Batman makes a deal with Mr. Whale, who brings him to Ghul. Ghul and Batman fight while Lt. Gordon and Barbara hack and disable the Ion Cortex. Batman then releases the souls from the sword who take Ghul away. Katana sees her father one last time before he leaves. Alfred leaves to set his wrongs from his past life's right, while Batman and Katana set out to continue saving Gotham.

A mystery being known as "the Golem" starts stopping crime in the district of Old Gotham. While in patrol, Batman and Katana find the Golem and begin chasing him. They eventually find out Rex Mason is the Golem and team-up with him to combat an army of armored thugs that have been terrorizing that neighborhood. In addition, they also dodge Harvey Dent's newly created Special Crimes Unit, which has been ordered to take down both the armored criminals and the vigilantes fighting them. After the failed attempt to capture the vigilantes, Dent is approached by Anarky to help bring down Batman. Batman figures out that it was Sapphire Stagg who gave the thugs their high-tech equipment. He warns her that she does not want be his enemy. She asks if the Golem is Rex, but he denies it.

The Key, a master thief, steals the most valuable piece of code-breaking software in the world. He is later arrested by Harvey Dent and sent to jail. With Key at Blackgate Penitentiary, Batman has himself arrested to recover the dangerous software. Before imprisoning him, Dent decides to let Batman keep his mask on, as an unbearable high-pitched frequency is emitted whenever someone tries to remove it. The Key is taken hostage by the prison's "king", Killer Croc. In order to get to the Key, Batman has to fight Killer Croc and his friends. The constant string of fights finally gets the best of him, as he beats Croc senseless. He is about to mindlessly kill Croc when Katana arrives and halts him. After cooling down, Batman convinces Key to cooperate. Nearly scared to death, Key agrees. The police then arrive and Killer Croc escapes into the sewers, plotting his next move. Back at Wayne Manor, Bruce is badly hurt from his encounter. As he lays in bed, Alfred returns home to look after him.

In order to keep his enemies closer, Bruce Wayne befriends Harvey Dent and the captain of the SCU, Dane Lisslow, with whom he makes a strong connection. Wanting to become mayor, Dent tries to win Bruce's financial support. Their meeting is cut short when Bruce sees what looks to be a giant bat. Intrigued, he starts investigating and finds out that, recently, there have been break-ins at several chemical facilities. This all seems to be connected with Professor Pyg and Toad who seem to be after samples of animal DNA. At one of the facilities, Batman and Katana encounter the Man-Bat creature. After a chase, Batman knocks him out and takes him to the cave. There, they learn that Man-Bat is actually scientist Kirk Langstrom. He became a monster when Pyg and Toad injected him with a serum of his own making. The two are kidnapping civilians to create an army of human-animal hybrids. Kirk teams-up with Batman and Katana to stop the experiments. After a fight, the villains are sent to prison, and Man-Bat decides to keep looking for a cure to his condition. At the mansion, Bruce agrees to support Dent to keep an eye on him.

Scientist doctor Sprangle is attacked by two Manhunters, super soldiers sent by The Council, a mysterious organization. They then attack Ava Kirk, but she is saved by Bruce and Katana and taken to the mansion for safety. She agrees to stay there, as Bruce is an old friend. While investigating, the heroes find a warehouse full of Manhunters. Paul, Ava's father, then appears and disintegrates them. It turns out that the Council cloned him to build an army of Manhunters. Doctor Sprangle worked there and freed Paul after discovering what was going on. Meanwhile, the clones break into the mansion and kidnap Ava. They are controlled through a neuron network, which also allows the Council to communicate with Paul. They tell him that if he ever wants to see Ava again he must come alone to the Gotham Bridge. With Ava's life threatened, Paul decides to surrender himself, but it all turns out to be a ruse that ends up saving Ava and imprisoning an important member of the Council. Still having to destroy the Council, Paul says good-bye. Before leaving, he asks Batman to watch over Ava. Batman agrees.

Harvey Dent faces off against Anarky as Batman and Katana fight their way out of a building surrounded by the GCPD. Meanwhile, Deathstroke makes his escape in the Batmobile, finds the Batcave, takes Alfred hostage, and issues Batman an ultimatum: if he ever wants to see Alfred alive again, he must come to Wayne Mansion alone.