In order to track The Key, a thief who has stolen a dangerous piece of code-breaking software, Batman has himself arrested and thrown into Blackgate prison. However, the prison's "king", Killer Croc, is also interested in obtaining the Key, and organizes a large prison riot to obtain him and get rid of Batman.

Ava Kirk, an old friend of Bruce Wayne's comes to him for help, when her father, Paul, has been cloned by The Council, a mysterious organization to create an army of super soldier Manhunters.