Gotham begins with a little torture as Theo Galvan has kidnapped the Mayor and held him hostage. He has a box around his head and threatens to drop a spider in it if he does not call and lie to his secretary and tell her that he is leaving town with his lover. He declares Gotham is about to be “cleansed.” The Mayor complies and news spreads quickly to headlines. At the Gotham Gazette, the editor declares he wants a better headline and demands his writers bring him new stories. As he rants people are seemingly falling from the sky behind him. We see the escaped Arkham inmates led by Jerome are tossing hostages off the building, lining their bodies up to spell out “M-A-N-I-A-X-!” At the precinct Jim and Sarah brief the cops on the inmates and prepare to go after them. Theo commends the inmates on a job well done and then tries to teach them about showmanship. All of them, save Jerome, fails. Theo applauds his laughter, while his sister and Barbara whip the Mayor. He stops them, but they tell him they are bored and want to participate in the “fun.” He questions her about Jim Gordon.
Back at the manor, Bruce and Alfred explore his father’s cave. He believes his father’s computer holds information on Wayne Industries and what could have led him to his death. Alfred destroys the computer, telling him he is trying to protect him. He, in turn, furiously fires him and tells him to never return. Jerome and the cannibal clash over who is more dangerous. Theo realizes he has to settle their rivalry once and for all and gives them a gun to play Russian Roulette with. The cannibal pulls the trigger once, but Jerome foolishly pulls it three times, proving he is deadlier than his compatriot. Theo makes him captain of the team for his insanity. Jim goes to visit Harvey and tries to get him to become a cop again, but the latter’s girlfriend forbids it. Harvey agrees with her, but points him towards the shipyard, finding it conspicuous they would have chosen that particular area to do the murders. Jim follows his lead and manages to get a license plate on a vehicle stolen from there. Sarah cannot believe Harvey has retired, she declares she will not waste her position as commissioner and declares it is a new day. At the Manor, Alfred and Bruce bid each other farewell. Elsewhere, Jerome and the inmates target a school bus full of cheerleaders!
At the precinct, Ed continues to try and woo Ms. Kringle, but fails. He kicks himself for not asking her out, and then argues with his darker self over pursuing her. Jerome and his men take over the bus and chain the girls down to their seats, forcing them to cheer at gunpoint. They then douse them in gasoline and try to set the bus on fire. The police try to stop them, but one of the inmates manages to start a lighter. Jim punches him out and then drives the bus away from the gasoline. He returns to interrogate the inmate, but Tabitha shoots the man before he can be grilled. Bruce sits with Alfred at the train station. There, he tells him he does not want him to go, but he will not stop trying to find out what is going on with his father. He tells him he is either with him or against him and demands he train him. Alfred agrees, but tells him he must do exactly what he says, when he says it. Bruce agrees, but only if he fixes the computer. At the precinct, the Sarah, Lee, and Jim discuss their findings from the inmate’s autopsy. Later, Alfred meets up with Lucius Fox and enlists his confidence and help with Bruce, promising him he will kill him if he turns on Bruce. He also gets his help fixing the computer.
Barbara calls Jim to try and toy with him. He tries to get her to turn herself in, but soon realizes she is there in the precinct. Jim goes after her. The inmates break into the precinct and open fire on all the cops and hold Sarah hostage. Ed barely manages to save Ms. Kringle while Lee hides out in her lab. Jim tries to get Barbara to be rational but she sicks one of the strong inmates, Aaron, on him. He beats Jim to a pulp! She declares she is not sick, but free and leaves. Jerome taunts Sarah and kills the cannibal for stealing his line. Jim regains consciousness and makes his way back to the precinct. He and Lee find Sarah dying from her wounds from Jerome. She tells him again, before dying, it is a new day. Lucius attempts to rebuild Thomas Wayne’s computer while Bruce questions him. He tells him it will take some time to repair it. Lucius tells Bruce he loved his father and regrets he never told him or helped him more. Bruce and Alfred receive word about the massacre at the precinct and go to check on and apologize to him. Later, Harvey returns to the force. Their reunion is interrupted by a broadcast from Jerome, warning them the worst is yet to come.