Unknown to Batman, however, Department of Justice member Amanda Waller was secretly observing the riot, to find potential recruits for a unit she was forming. After saving her from them, Batman and Catwoman formed an uneasy alliance to save the hostages trapped in the Arkham Wing of Blackgate, which required Batman to locate codes at the Industrial, Administration, and Cell Block wings of Arkham, which were controlled by Black Mask, the Joker, and the Penguin, respectively. Upon infiltrating, Batman encountered Catwoman being surrounded by three thugs, each representing the Penguin, the Joker, and Black Mask. Six hours later, Gordon notified Batman (who had listened to the police scanners) about what was going on, with Batman deciding to infiltrate via the riverside, even though it was a impregnable wall that way, and Batman being aware of the risks of quelling a riot instigated by criminals of every stripe who had more than enough of a grudge against him. Two weeks later, a mysterious explosion occurred at Blackgate Prison, resulting in an immense riot occurring at the facility that placed the entire staff hostage. He then left her to the GCPD who had the area surrounded. Upon cornering her at a construction site and defeating her, he learned that Catwoman had already managed to upload the data she stole to her employer, and even she doesn't know what the data was. However, he was forced to deal with both Catwoman and the Omega Squad of the Department of Extranormal Operations who were also after the data, the latter group under the belief that Batman was an ally of her. One night in Gotham City, he witnessed a catburglar named Catwoman breaking out of a building with stolen data, and confronted her. However, several criminals were also challenging Batman, forcing him to keep himself one step ahead. Three months had passed since the events at Blackgate, and Batman had effectively become feared among the criminals.

Batman: Arkham Origins Blackgate is a completely separate experience that takes place after the events of Arkham Origins inside Blackgate Penitentiary.

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