A master thief known as The Key has stolen the most valuable piece of code-breaking software in the world. Batman and Katana try to retrieve the software from him, but he is arrested before they can catch him, by Harvey Dent. The Key is sent to jail, despite Batman's warnings that sending him to prison with the code is a bad idea, for Dent's new Anti-Vigilant Force is looking at him in a bad light. With Key at Blackgate Penitentiary, Batman tricks Katana into thinking he is going to bed, so he can find a way into Blackgate. When Katana decides to sleep as well, Batman has himself arrested and sent to prison to recover the dangerous software. There, Dent and the police try to remove his mask. However, a high pitched frequency is emitted. They plead for him to stop it, and he complies. Dent decides to let him keep it on, for with his costume, the other prisoners are more than likely to try to kill him. Gordon soon finds out that Dent has arrested Batman, and takes action by announcing that he will barge in with non-lethal force. With the mayor supporting Dent, however, he is forced to stand down. Unfortunately, the Key has been taken hostage by the prison's "king", Killer Croc. After freeing himself from handcuffs, Batman now must now fight his way through Blackgate's entire prisoner population, while Katana works with Commissioner Gordon and Oracle a.k.a. Barbra Gordon to save him. In order to get the "Key," Batman has to fight Killer Croc and his friends for it. Outside, Oracle helps Katana get into the prison through several underground tunnels. As Batman fights, a newly arrived Tobias Whale gives him tips on his opponents, allowing him the advantage to defeat Killer Crocs fellow inmates. Gordon pressures Dent to take action by threatening to go to the media, telling them that it's Dent's fault that they aren't doing anything. As Batman continues fighting Croc, he notices a skin rash, and uses it to his advantage to overpower Killer Croc. Unfortunately his breakdown finally gets the best of him, as he beats Croc senseless, severely damaging his body. Quickly, Katana arrives and halts Batman from mindlessly killing Croc. After cooling down, Batman tells Key to cooperate or he's next. Nearly scared to death, he agrees. Some of the prisoners want to still fight Batman, but before they can, the police arrive, and the two leave. Gordon tells Batman and Katana that everyone is unharmed, the prisoners are being reprocessed, and the Key wouldn't be a problem anymore. Gordon says that he thinks Batman scared Key, also commenting that Batman should see a doctor. He denies it and walks away. Katana then explains to him she knows what he needs, and follows him home. Meanwhile, Killer Croc has escaped into the sewers, plotting his next move against Batman. Back at Wayne Manor, Bruce is badly hurt from his encounter, and as he lays in bed, Alfred returns home to look after him.
Note: Penguin is referenced by Harvey Dent and is seen on a wanted poster.