Jason Burr (who is still under Cypher’s control) steals the Ion Cortex for the League of Assassins as Lady Shiva brings Ra’s al Ghul out of suspended animation. Batman believes that he has turned to evil, but Katana does not. Batman, Katana, and Alfred then find themselves in a difficult situation as they battle the League of Assassins in a fight to save Gotham City from darkness. As they try to stop Jason from activating the Ion Cortex, Katana discovers that he is being controlled by Cypher. With Katana’s help, he breaks free, Batman promises to help him, but he has to help shut down the cortex.
Before he can do so, Lady Shiva uses the sword of souls on him, draining his soul into the sword. Both Batman and Kantana are captured, but Ra’s al Ghul allows Batman to fight him (all the while being plagued by memories of Alfred’s early lessons to him), and as a result of him losing is captured by Ra’s al Ghul, while Katana and Alfred are left scared and alone.