|01 "Pilot"||09 "Harvey Dent"||17 "Red Hood"|
|02 "Selina Kyle"||10 "Lovecraft"||18 "Everyone Has a Cobblepot"|
|03 "The Balloonman"||11 "Rogues' Gallery"||19 "Beasts of Prey"|
|04 "Arkham"||12 "What The Little Bird Told Him"||20 "Under the Knife"|
|05 "Viper"||13 "Welcome Back, Jim Gordon"||21 "The Anvil or the Hammer"|
|06 "Spirit of the Goat"||14 "The Fearsome Dr. Crane"||22 "All Happy Families Are Alike"|
|07 "Penguin's Umbrella"||15 "The Scarecrow"|
|08 "The Mask"||16 "The Blind Fortune Teller"|
- "These are electrode wounds. This man was given a crude, invasive kind of electroshock therapy. Metal needles were inserted into the brain and electricity was applied to his frontal lobes."
- —Dr. Thompkins to Officer Gordon
Det. Gordon’s assignment at Arkham Asylum gets off to a rocky start when the murder of a guard ignites an investigation, leading him to meet Dr. Leslie Thompkins. Meanwhile, Cobblepot continues to build his army.
Several weeks pass and Jim Gordon begins his job as a security guard for Arkham Asylum. One night in the middle of a coordinated play by a nurse, Dorothy Duncan, Frogman Jones loses his sanity and attacks one of the actors, Royston hitting him several times before Gordons and his cohorts manage to stop it. It being another altercation that he should have been prevented, Jim is reprimanded by Director Gerry Lang, who blames him for letting the situation happen in the first place. Moments later, Dr. Leslie Thompkins comes to the infirmary to inspect Royston and meets Jim. Meanwhile on the streets of Gotham, Selina finds Ivy sick sleeping in a box in the rain, so she decides take her to Barbara Kean's penthouse, assuming that this would be empty. The next day, the Penguin comes to the port in an attempt to raise the Fisherman's taxes without the authorization of Don Maroni, however a GCPD officer arrives having been called by the Fisherman, and knocks Penguin out and arrests him and Gabe.
Back at Arkham, amidst one of his rounds Gordon discovers a patient in a vegetative like state complete with a two holes on the side of his head. With the help of Dr. Thompkins, Jim discovers that someone had administered electroshock therapy on the patient, completely frying his brain. After being informed of the situation, Director Lang prohibits Gordon from alerting the police and gives him the task of finding out who committed such an act. As someone needed the keys from a guard to access the patient's cell, Gordon investigates his fellow officers, namely Steven Wenger, to discover which one of them lost their keys, with Wenger confessing that he lost his during the riot during the play the previous night. At Mooney's nightclub, Fish Mooney meets with Jimmy Saviano and Janacek, two other underlings of Don Falcone to find out how they felt after Falcone had raised their tariffs. Saviano stated that he wished something would happen to Falcone before any of them ended up like Bannion, and he asserted that he'd takeover if Falcone fell as if he was next in line, to Fish's dismay. Along with Nurse Duncan, Gordon interrogated several patients in the asylum, including Jack Gruber, a sociopath imprisoned for murder and rape, and Aaron Danzig an inmate who had murdered his entire family with an axe, who also lacked the concept of lying.
At her nightclub, Fish begins to make plans to deal with Saviano knowing that he would present an obstacle. However, Butch offers to handle the situation as him and Saviano had known each other since childhood, and as such had history together. At Arkham, Royston is abducted and subjected to electroshock therapy, like Frogman had been. Suspecting that perhaps it was a staff member doing so, though Lang suspects that Gordon is trying to force his hand to get the GCPD involved, but Gordon informs him that he already called them. Elsewhere, Barbara is told by Renee that them together was a toxic combination and that she needed to go back to Jim. However this didn't sit well with Barbara, who angrily got her stuff to leave, though Renee offered to go. Alerted by Gordon's call Bullock visited the Asylum, happy to see his former partner, but seeing as Lang refused to call it in, and he had the skills in order to perform electroshock therapy, Bullock takes Lang to the GCPD for questioning. At the port, Butch met with Saviano, who ended up asking him to drop Fish, and come work for him, offering him anything he wanted if he did so.
At the GCPD, Bullock is surprised to find the Penguin locked in a cell and refused to release him as he liked having him there, right where he could see him. Bullock then went on to interrogate Lang, asking him who on his staff could possibly do such a thing. Lang defended his staff members, telling Bullock that they had all been with him for the past 5 years and they had all come to Arkham together, except one person. Analyzing the blueprints of Arkham, Gordon discovers that the person who had been attacking the inmates should be based in the basement area, so Nurse Duncan offered to escort him there. On the way to the basement, Jim begins to notice her strange behavior, and the situation worsens when the two cross paths with Dr. Thompkins who offered to accompany them. Suddenly, Duncan pushes Leslie towards Gordon and begins to flee in terror. Soon after, Harvey calls Gordon to inform him that Dorothy Duncan was actually a patient and not a nurse. In her desperate attempt to flee, Dorothy Duncan opens all the cells in the asylum and starts a riot but unfortunately is killed when she falls and is walked on by man of the inmates. Jim and Leslie on the other hand, manage to gate the inmates off and save themselves.
That night Barbara calls her penthouse to talk to Jim, but Ivy answers the phone, lying, telling her that she was a friend of Jim's, and that Jim was busy. At the GCPD, Gordon and Bullock reported to Captain Essen what had happened and how Duncan had stayed in the basement of Arkham when it originally closed, disguising herself as a nurse when it was re-opened. With another case finally solved the trio shares a drink for old time's sake, but are interrupted when the Medical Examiner come in to tell Essen that he had found electroshock therapy marks on Duncan's head as well, proving she was not the culprit after all. Outside the room, Maroni arrives at the GCPD, revealing he had Penguin locked up in order to teach him a lesson in humility, after trying to raise the Fisherman's taxes without asking him first. At that very moment, Aaron releases himself from his cell with the stolen keys and kills Officer Wenger on the orders of Jack Gruber, who had been behind the attacks from the start. Arriving at the Asylum, Gordon finds a note from Gruber in the hand of a dying Director Lang, in which he expressed his wishes for the two to meet again. The next day Jim returns to Barbara's penthouse where he finds evidence that someone had been staying there. At the port, Butch once more meets with Saviano to tell him his answer. Butch agrees to join up with Saviano, and after telling his old friend how he had cheated him out of angus steaks when they had robbed a deli as kids, Butch killed him.