April, 1986: Batman, having returned to active duty in Gotham City, is called in by Commissioner James W. Gordon to capture the escaped Crazy-Quilt and Signalman, who are trapped in a warehouse. The Gotham City Police Department moves to a new building. Batman recalls the last five months. In October, Ra's al Ghul engineered a mass prison break of all of Gotham's criminals, and just after Batman and his allies recaptured the worst of them, the Swamp Thing attacked the city. Shortly after, while on the trail of the Black Mask, Batman became overwhelmed by the loss of the last few months and had a breakdown. Temporarily retiring as Batman, he refocused his energy as Bruce Wayne to help lead Gotham City's restoration and began recruiting six heroes for a new Secret Six team to recapture the remaining prison escapees. In December, Batman rejoined the Outsiders and encouraged Robin II to join the Titans, temporarily leaving the problems of Gotham to the GCPD and his new team, the Secret Six. [“Batman: Gotham Knights, Chapter 1: A Loss of Faith”]
Batman moves in to recapture Crazy-Quilt and Signalman. Robin II (Jason Todd) returns from a case with the Titans. Alfred Pennyworth presents Robin II with a new costume that has a cowl, allowing him to stop dying his red hair black. Robin II receives a package delivered to him through the GCPD. Batman captures Signalman. Robin II learns that Nocturna (Natalia Knight), missing since the Crisis, is still alive and being held in the Middle Eastern nation of Qurac. [“Batman: Gotham Knights, Chapter 2: Unmistakably Robin”]
Batman captures Crazy-Quilt and comes up with an idea to put an end to Gotham City's plant problem. Returning to the Batcave, Batman begins working on a plan to use Mister Freeze's ice gun to remove the last of the aggressive plants from the city. Hours later, Batman and Alfred realize that Robin II has disappeared. Batman realizes that Robin II has gone after Nocturna in Qurac and taken the Batplane there. [“Batman: Gotham Knights, Chapter 3: As Night Follows Day”]
Batman asks Batwoman, Man-Bat, and Ragman to protect Gotham City in his absence and directs them to use Mister Freeze's ray gun on a new lighthouse dome assembly against the plant growth. Bruce Wayne takes a private jet to Lisbon, Spain, to track down Robin II and the Batplane. Robin II arrives in Qurac and parachutes down to find a circus there. Over Greece, Batman explains to Alfred that the pilots think he is traveling under disguise as Bruce Wayne to Qurac; Batman arrives in Qurac in a small, ultralight plane. In Gotham City, Batwoman, Man-Bat, and Ragman affix Mister Freeze's ice gun to the lighthouse dome and begin using it to clear Gotham's plant growth. [“Batman: Gotham Knights, Chapter 4: Send Out the Clowns”]
In Qurac, Robin II awakes to find himself in a TV studio as a prisoner of the Joker and sees the unconscious Nocturna there as well, having been the Joker's prisoner for months. The Joker begins a game show called “Who Wants to Knock Off a Superhero's Mother?” Batman arrives at the same circus and begins searching for Robin II. Broadcasting worldwide, the Joker has people call in and vote to save or to kill Nocturna. Robin II begins trying to escape. [“Batman: Gotham Knights, Chapter 5: 1-800-EXECUTE”]
Batman enters the TV studio and heads for the control room. Robin II escapes and attacks the Joker, while Batman finishes rigging the call-in poll in favor of Nocturna's life. In Gotham City, Dick Grayson (Nightwing) returns to the Batcave. In Saudi Arabia, Batman and Robin II learn that Qurac won't allow them to take the Joker back to the U.S. and that Nightwing has returned to the Batcave. Robin II flies the Batplane with the unconscious Nocturna back to Gotham City, followed by Batman in the private jet. Robin II worries that Nightwing will want his old role as Batman's partner back. In the air approaching the East Coast, Batman witnesses the apparent destruction of the Daily Planet building in Metropolis. [“Batman: Gotham Knights, Chapter 6: Homecoming”]