Batman: Arkham Asylum After the Joker assaults Gotham City Hall, he is caught by Batman and taken to Arkham Asylum, which temporarily houses many members of the Joker's gang, who were transferred after a fire at Blackgate Prison. Believing the Joker allowed himself to be captured, Batman accompanies him into the asylum. The Joker's plan is revealed as Harley Quinn takes control of the security and the Joker escapes into the facility, aided by a corrupt guard who kidnaps Commissioner Gordon. The Joker threatens to detonate bombs hidden around Gotham City if anyone tries to enter Arkham, forcing Batman to work alone. Tracking Quinn to the medical facility to rescue Gordon, Batman is exposed to the Scarecrow's fear toxin and hallucinates, seeing Gordon's death and the corpses of his parents talking to him. After fighting off Scarecrow, Batman finds and subdues Quinn before rescuing Gordon. The Joker then directs Batman to the captured Bane, who has been experimented on by asylum doctor Penelope Young. The Joker frees Bane and Batman is forced to fight him, during which Quinn escapes. Afterward, he goes to a secret Batcave installation he had hidden on the island, where Batman restocks his gadgets.

There, Batman learns that the Joker returned to the asylum to gain access to Young, who has been developing Titan—a more powerful version of the Venom drug that gives Bane his strength—intending to use it to help patients survive more strenuous therapies. Young learned that the Joker had been funding her research to create an army of superhuman henchmen; her refusal to hand over the formula precipitated Joker's return to the Asylum. While searching for Young, Batman is again attacked by Scarecrow and the fear toxin, and hallucinates the night of his parents' deaths. After he recovers, Batman destroys Young's Titan formula and rescues Young from Victor Zsasz. An explosion kills Young and the Joker obtains the completed batches of Titan.

Batman: Arkham City The events of Arkham City are set one year after Batman: Arkham Asylum. Quincy Sharp, the asylum's erstwhile director, has taken sole credit for halting the Joker's armed siege, using this distinction to become mayor of Gotham City. Declaring both the asylum and Blackgate Penitentiary no longer suitable to contain the city's detainees, Sharp's administration orders both facilities closed and he purchases Gotham's most notorious slums, converting them into an immense prison enclosure known as Arkham City. This facility is subsequently placed in the care of psychiatrist Hugo Strange—who is secretly manipulating Sharp—and monitored by a rogue private military firm, TYGER Security. Strange permits the inmates to do as they please, so long as they do not attempt to escape. A wary Batman maintains his own vigil over the new project, concerned that the chaotic situation there will get out of hand. Meanwhile, the Joker is suffering from a potentially fatal disease caused by his previous consumption of the Titan formula, an unstable steroid serum which turns men into maddened monsters.

At a press conference held by Bruce Wayne to declare his opposition to Arkham City, TYGER mercenaries arrest and imprison him in Arkham City. Hugo Strange discloses his knowledge of Wayne's dual identity as Batman before releasing him into the prison's criminal populace. While Strange prepares to commence "Protocol 10", Wayne obtains his equipment via airdrop from Alfred Pennyworth, allowing him to become Batman. He first saves Catwoman from being executed by Two-Face, who hopes to gain respect by murdering her. After Joker attempts to assassinate Catwoman, Batman tracks him to his hideout in the Sionis Steelmill, believing Joker may know the truth behind Protocol 10.