Jason Burr, still not in control of his body due to mind control by Cypher, steals the Ion Cortex in order to make a deal with the League of Assassins.
A Golem creature has been fighting back against armored criminals attacking local businesses. Tracking the creature down to an abandoned synagogue, Batman and Katana discover that the "Golem" is actually Rex Mason.
After his ordeal at Blackgate Prison, Batman is haunted in his dreams by a mysterious winged humanoid bat, only to later discover that he really exists. Meanwhile, Alfred returns and tries to help Bruce work out his personal issues.
An old friend of Bruce Wayne's comes to him for help, when her father has been cloned by a mysterious organization to create an army of super soldier manhunters.
When Batman and Katana are ambushed in the Gotham subway by Killer Croc, it's up to Barbara Gordon to save them. Only one problem: Barbara's on a date.
Batman continues to work in secret to find answers, while Harvey Dent recovers in Gotham Hospital. Blaming Batman for everything, he enacts martial law in Gotham.