Busting into the Joker's hideout, he encounters the Joker seemingly dead, only to be ambushed by the clown and knocked unconscious. With her safe, Batman jury rigs a new device, the Remote Electrical Charge and goes after Quinn and the Joker. As they drag away the doctor, Batman makes his entrance and goes to rescue the doctor. Making his way inside, Batman discovers another doctor at the mercy of the Joker's goons for being unable to heal him. The entrance blocked, Alfred ruefully realizes that Batman's going in the only other way - the chimney pipe. His search leads to Sionis Industries Steel Mill. He escapes from the tower and begins tracking down the Clown Prince of Crime through radio frequencies. Investigating the church further, Batman discovers where the sniper post was located - along with a lot of explosives. As Harley escapes, Batman's able to rescue the hostages and take down the thugs. Pinpointing the source to a church, he goes to investigate, encountering Harley Quinn and a number of Joker thugs, all of which have taken hostages. However, as the two are talking, Batman ends up saving her again from a sniper. Sneaking in, Batman is able to subdue Two-Face and rescue Catwoman. His first stop is at the Courthouse, where Catwoman is being held captive by Two-Face. However, he's able to escape for good and, after contacting Alfred, is able to get a canister delivered containing his Batsuit. One attempt to escape leads to his recapture and he is soon thrown into the hands of the Penguin. Hugo Strange, the warden of Arkham City, who gleefully lets Bruce know that he knows his secret identity. A year has passed and Bruce Wayne, wanting to know what is going on inside, makes himself known and speaks out against Arkham City, leading to a squad of TYGER guards that arrive and arrest him. To solve this problem, Quincy Sharp, the former warden and now mayor of Gotham City, has created a new location: Arkham City, using the slums of Gotham as his holding grounds. In the aftermath of Batman: Arkham Asylum, the titular asylum is ravaged and there's no where to put the villains left unchecked.

Mad hatter batman arkham city