Batman: Arkham Asylum The game begins with Batman escorting the Joker in the Batmobile to Arkham Asylum after catching him at Gotham City Hall.

The situation at City Hall took place at the exact same time as a 'mysterious fire' at Blackgate Prison, causing many of the prisoners to be sent to Arkham, among them a great number of Joker's own gang. When the two arrive at Arkham, Batman and several helmeted security guards strap the Joker to an upright stretcher and wheel him down into the Intensive Treatment Center. Batman accompanies the security personnel and the Joker to the Holding Cells, where the Arkham staff refuse to let Batman go any further. As the Joker is being registered into the Cell Block by Commissioner Gordon, he breaks free from a guard and escapes from Batman with the help of Harley Quinn. Batman, who is locked out of the area, breaks into the Holding Cells through a glass window. Once Batman is inside the Holding Cells area the Joker springs his first trap, unlocking the cells and allowing Blackgate convicts to flood out to attack Batman. After another brief confrontation with more convicts, the Joker deactivates a security gate, allowing Batman to follow after him despite Commissioner Gordon's observation that it was most likely a trap. Batman moves up a ramp in the direction of the Joker's escape, leaving the Holding Cells and entering the Processing Corridor, finding the hallway littered with fallen security guards the Joker left in his wake. He found one guard that had survived named Eddie Burlow, who points him to the Lower Corridor. Batman reaches the Patient Pacification Chamber, where two security guards inform him that escaped inmate Victor Zsasz has taken another guard, Mike, hostage and will kill him if he sees Batman get close to him. Batman subsequently subdues Zsasz after swooping down from a gargoyle. All of a sudden, Batman receives a message from Harley Quinn, who has taken Quincy Sharp, the warden, hostage. Although Quinn is convinced Batman is trapped in Patient Pacification, Batman escapes back to the Processing Corridor, moving into the Decontamination area, where several Arkham personnel and inmates were trapped in a room filling with Joker Toxin.

Batman: Arkham City Prologue New Arkham City inmate and rising warlord, Two-Face devises a plan to publicly execute fellow prisoner Catwoman after she tries to steal back some of her ill-gotten gains from his hideout. Meanwhile, Gotham City itself has degenerated into a police state managed by Mayor Sharp, where citizens with the slightest trace of a criminal record find themselves shipped to the prison district. Those who dare to challenge Sharp's policies are the target of arranged disappearances, becoming political prisoners trapped behind Arkham's walls. Among these is Bruce Wayne, who holds a rally attacking the proposal of turning half his city into a walled-off reserve for criminally inclined persons. Segregated from society, he argues, they have become responsible for their own survival in an anarchic urban hell which is characterized by bloody gang wars.

Welcome to Arkham City Wayne, as the latest focus of Sharp's vendetta, is kidnapped by TYGER Security operatives working for Hugo Strange, who is privy to his dual identity as Batman. Strange intends to unveil new plans for Arkham City before the night is up, an operation codenamed Protocol 10, which will establish himself as supreme ruler of Gotham. Now an inmate, the Dark Knight manages to have Alfred Pennyworth deliver his crimefighting equipment to him directly via an airdrop, and he prepares to save Catwoman from Two-Face for the sake of their past relationship while uncovering the true nature of Protocol 10.

Batman: Arkham Knight Prologue Nine months after the |Joker's death, crime rates in Gotham City have dramatically declined, but Batman anticipates a new threat and maintains a vigil over the city. Before his death, the Joker sent his mutated blood to Gotham's hospitals, and several patients were infected. While most were cured, the patients who were not treated are starting to look and act like the Joker. Batman researches a cure for the mutations, and orders Robin to watch over the infected.

The Arkham Knight On Halloween night, Scarecrow unleashes his newest strain of Fear Gas in a diner, and threatens to release it throughout Gotham. Six million civilians are evacuated, but the city's criminals and supervillains stay behind, leaving Commissioner James Gordon and the Gotham City Police Department outnumbered. Batman investigates Scarecrow's presence, and searches for him in a rooftop safehouse, but instead finds and saves Poison Ivy, who was being held captive by Scarecrow's henchmen. In a makeshift Batcave in Gotham's Clock Tower, Barbara Gordon is collecting information on Scarecrow's new toxin, and traces its production to Ace Chemicals. Batman goes to investigate, but is confronted by the mysterious "Arkham Knight" and his militia, which has a massive army of unmaned tanks. Batman fights his way through the militia, learning from workers that Scarecrow is planning to produce a chemical explosion so large that it will cover the entire eastern seaboard in fear toxin. Batman reaches Scarecrow, who reveals to him that Barbara has been abducted by the Arkhan Knight before escaping. While reducing the blast radius, Batman is exposed to the fear toxin, which reacts with his own mutated blood to cause hallucinations of the Joker. Escaping from the exploding Ace Chemicals, Batman is forced to tell Gordon about his daughter's involvement in his crime-fighting, and the outraged Gordon swears that he will find Barbara without Batman's help.

Scarecrow's Plans Batman tracks the Arkham Knight to an underground tunnel network, hoping to learn Barbara's whereabouts from him, but instead gets ambushed by him. Batman then gives chase to the escaping convoy, only to learn that the driver is a decoy, using a voice synthesizer that makes him sound like the Arkham Knight. Batman interrogates the driver and learns that they are heading to the North Refrigeration. He and Nightwing interrogate the Penguin, who tells them that the Knight and Scarecrow are meeting with a businessman named Simon Stagg, who runs a pharmaceutical company. After boarding Stagg's airship, Batman discovers that Scarecrow paid Stagg to create a device known as the "Cloudburst", but Stagg tried to double-cross them and has been doused with fear toxin as punishment. After reaching Scarecrow and interrogating Stagg, Batman is again exposed to the toxin, which triggers a powerful hallucinogenic response. Scarecrow escapes with the Cloudburst. Batman receives a message from Scarecrow revealing that Barbara is in the same safehouse where Ivy was held, but before Batman can save her, Barbara is doused with fear toxin and shoots herself in the head. Batman and Alfred Pennyworth are devastated, but Alfred convinces Batman to not lose hope, for Barbara's sake. Alfred explains to Batman that the Cloudburst is a dispersal device designed to flood all of Gotham with the fear toxin. To counteract this effect, Batman enlists the help of Ivy, who takes control of a large tree which develops giant flowers capable of neutralizing the toxin.