In Gotham City, Scarecrow unleashes a toxin gas at the ceremony for the new mayor and most citizens there die or are affected by the gas. Batman takes down Scarecrow and his crew before being affected to the gas. Scarecrow joins alliances with Joker inside Arkham Asylum and vows to take down Batman.
Later, Black Mask stages a large breakout at Arkham Asylum and starts leading his forces to take on the GCPD and Batman. Batman starts his mission to round up all of his villains and stick them back in Arkham Asylum. First, he finds Victor Zsasz about to kill a politician near Crime Alley and takes Zsasz down.
Penguin launches missile attacks from the Iceburg Lounge on Gotham City and kidnaps Nightwing and Robin (Tim Drake), forcing Batman to find them both. The Dark Knight also barely escapes Black Mask's ongoing onslaught on Gotham and gets to Penguin in time. The Caped Crusader finds out that Penguin has stolen missiles from the military, including a specially designed chemical weapon, even deadlier than Scarecrow's fear gas. Batman rescues both of the heroes and locks Penguin up.
Batman intercepts a message from Joker and Scarecrow, telling him to meet them at the Sionis Steel Mill.