The episode opens as last season ended: With Alfred and Bruce walking down the stairs hidden behind a fireplace in Thomas Wayne’s office. They come to a heavy metal door with a Medusa-like design on it and a keypad that requires a five-digit combination. Bruce starts trying combinations, but is discouraged when Alfred tells him there are too many to try them all.
At Jim Gordon’s apartment, Leslie Tompkins helps him get ready for work as a uniformed cop. Elsewhere, Bullock tends bar. At another, palatial location, Penguin has Victor Zsasz kill someone for him and smiles as other mob bosses wince. At Arkham, Barbara Kean is admitted, much to Jerome’s excitement.
Elsewhere, a man in a helmet, wearing body armor, swords and a cape drinks a strange liquid given to him by a well-dressed man and laughs. That same man steps out onto the streets later with guns, firing them indiscriminately and calling himself “Zaardon,” spewing a nonsensical, self-aggrandizing monologue. Gordon disarms him of his guns, but the man pulls a sword and takes a bystander hostage. When he throws the hostage away, Gordon tries to talk him down rather than shoot him. Ultimately, he has to wrestle the man to the ground and handcuff him.
As he’s wrapping up, his new partner arrives, late for his shift and eating, and frustrated when Gordon is stressed out about it. Jim pushes him and then stops a number of passersby from looting a roadside vendor whose table had been knocked over in the struggle.
Back at the police department, Gordon books Zaardon, who can’t understand how he was overtaken even after having drank from “the chalice.” Gordon puts him in a holding cell, while the man threatens him and continues to rant.
In the locker room, Gordon sees Eddie Nigma, but before they can talk much, Gordon is distracted by noise outside and leaves. After he does so, Nigma’s reflection starts talking to him, mocking him and telling him that he needs to be more confident and have more fun. He begs his reflection to leave Miss Kringle alone, but the reflection isn’t impressed. When he puts his glasses back on, the reflection does not, and then laughs.
In Essen’s office, Loeb fires Gordon for having pushed his partner. Essen objects, but Loeb isn’t interested. After surrendering his badge and gun, Gordon assures Loeb that he’ll still take him down.
In the holding cell, a sleeping Zaardon burps, and a cloud of blue smoke comes out of his mouth.
At home, Gordon and Lee talk about the situation in bed, with Lee saying maybe it’s for the bed. Jim says that there is still recourse, even though he doesn’t have any legal moves left.
At Arkham, Jerome introduces himself to Barbara, telling her that Richard Sionis is interested in her. She’s unimpressed, until Jerome suggests to her that a girl needs a friend for protection in Arkham. She calls a huge man over, flirts with him and convinces him to be her friend. Jerome is impressed, but tells her that Sionis can get her things. She asks for a phone.
At Penguin’s table, Butch tells Penguin about a debtor who refuses to pay because he owes Falcone, not Penguin. Selina is there, and acknowledges Gordon’s greeting. As Penguin is talking about how this unacceptable, Gordon enters. Penguin guesses that Gordon wants Loeb fired and his job back, and tells him that he’ll do it, provided Gordon collects a debt for him first. Gordon refuses.
Gordon goes to the bar where Bullock works, and drinks his problems away. Bullock is sober, he’s happy, he has a fiancee. He suggests maybe Gordon should consider the merits of civilian life. The two hug and Gordon leaves.
Gordon goes to Wayne Manor to admit he’s been fired and that he will fail to catch the Waynes’ killer. He admits to Bruce that he would have to get into bed with Penguin to get his job back, and Bruce tells him that he must do it. Alfred is frustrated with Bruce and tells him there’s a lot he doesn’t understand since he’s a child. Bruce apologizes to Gordon and Alfred sees him out.
Bruce goes back and keeps poking away at the combinations on the keypad, then gets frustrated and bashes the keypad to pieces with a hammer.
At Arkham, Barbara approaches Sionis about the phone.
Gordon, unsurprisingly, goes straight to Barker, the man who owes Penguin money. Barker refuses, saying that Penguin won’t last a year. He tells Gordon to leave, threatening to shoot him when he doesn’t leave right away. Gordon says he’ll count to three, but after one, he takes the gun and knocks out almost everyone in the room, holding a gun on the last man to fill a bag with money. Barker and his people chase Gordon outside, where they shout “stop, thief” and a trio of beat cops join the chase. Gordon slips all of them but is nearly gunned down by Barker in a parking garage, instead killing Barker.
At Wayne Manor the next day, Bruce is setting up explosives to break into the underground room. Alfred is furious, but Bruce tells him that he’s going to do it one way or another, and that with Alfred’s help at least the bomb would be safe. Alfred agrees to help.
Gordon brings Penguin his money, accusing him of knowing that Ogden would go off. Penguin denies it, and Butch looks confused/stoned.
At home, Lee is talking to Jim when Barbara calls. She tries to tell him that Lee was the one who attacked her, that Lee is crazy and that she never admitted to calling her parents. When Gordon won’t tell Lee who called, the house phone rings. It goes to the machine, and Barbara leaves a threatening message. Lee suggests they leave Gotham and never come back, prompting Jim to admit that he did the bad thing he had hinted to her about earlier.
Commissioner Loeb wakes up in his bed, hears a noise and finds Zsasz and Penguin in his home. They’ve already killed his security detail and tell him that they’re going to kill him, eventually offering him an out: reinstate Gordon, retire and leave Gotham, never to return.
Cut to his retirement press conference, in which Loeb names Essen as his successor. Mayor James couldn’t attend, but sends Theo Galavan in his stead, who delivers a farewell speech for the commissioner. Galavan is, in fact, the man who had given Zaardon his potion earlier in the episode.
At Arkham, Barbara has made herself comfortable, with Sionis and the others waiting on her hand and foot (literally — there’s a dude giving her a pedicure). As they’re talking, Zaardon comes in and starts shouting. They’re unimpressed, until he collapses in the middle of a rant and apparently dies, blowing out a plume of blue smoke. The gas knocks out all the inmates in the room, and then a group of well-armed, leather-wearing people in gas masks storm in, kill the guards and eye the room.
Back at the police department, Commissioner Essen tells Gordon it’s a new day, and they’re going to do great things. Gordon tells Lee that things will be alright, and Lee says she hopes it was worth it.
Essen, who had been called away, returns to say that Barbara is among six inmates who have escaped Arkham.
The inmates wake up in Galvan’s penthouse, where he and his sister — one of the terrorists who stormed Arkham — are giving them the hard sell: Come work for him. Team up to bring the city to its knees.
Sions isn’t interested, and tries to lave, but Tabitha Galavan kills him instead, using a whip and then a knife. The whole time, Jerome laughs. Now, the rest of the “team” is sold on Galavan.
At Wayne Manor, Alfred and Bruce hide behind a heavy piece of furniture and set off the explosives in the cave-room door. They head into the basement and find that inside of the formerly-sealed room there is a computer setup, and a note from Thomas telling Bruce (the combination to the door was “Bruce,” by the way) that if he’s found it, then Thomas is dead. He says that once he became a father, he wanted to be a better man and started asking hard questions about the family business. He says “you can’t have both happiness and the truth; you have to choose.” He begs Bruce to choose happiness, unless he feels a calling.