|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"|
- "You will be free of fear forever. You'll be cured. Are you ready, Jonathan? Are you ready, son?"
- —Gerald Crane to Jonathan Crane
Gordon and Bullock set out to stop Gerald Crane, a biology teacher who has been harvesting the adrenal glands of his murder victims. Meanwhile, after finding herself in an unusual setting, Mooney continues plotting to gain power, and Falcone attempts to change Maroni’s plan for the Penguin. Then, Bruce takes a treacherous hike.
During a storm, Gerald Crane and his son, Jonathan, terrified another victim after he arrived at his apartment. Elsewhere, Fish Mooney woke up in an unfamiliar place, surrounded by men fighting. She is soon approached by two men, who she gets to leave after threatening both of their lives. In the city, Jim and Leslie concluded their third date, with Leslie informing him that she was hired as the new medical examiner of the GCPD, much to Gordon's surprise. The next day, while the police search the home of the most recent victim of Crane, Bullock gives Gordon the rundown once he arrived. Elsewhere, Crane uses the adrenal glands to make a serum that he injects himself with. After doing so, he has hallucinations of his wife haunting him in the midst of a blazing fire. Meanwhile at Wayne Manor, Bruce prepares to leave to honor a yearly he and his father had of camping and watching the sunrise in the morning.
At Mooney's nightclub, Penguin tries to convince Don Falcone of Maroni's threat to his life, however Falcone continues to talk about the re-decoration of Fish Mooney's club, to Oswald's frustration. Falcone then tells Penguin that he has decided to give the club to Penguin as a reward and that he would deal with Maroni. At the GCPD, Leslie arrived at the GCPD for her first day, and using a school yearbook of the school that Gennaro Marx worked at, Bullock discovered Crane's identity. Meanwhile Fish discovers that the boss of the underground prison she was being held at was run by a prisoner named Mace, and Bruce began his journey hiking in the forest. The Detectives Aquinas High School intending on finding out information about Crane, and the headmaster, Judith Barthel informs them that Crane was very overprotective of his son Jonathan and that his wife died several years ago in a car accident. She also gives them an academic paper that Crane had wrote, where he explained his theory that the fear was an evolutionary failure in humans and was trying to cure himself of it. Back at the GCPD, Bullock and Gordon discover that Crane had intentions on creating inoculations for himself and another person, dubbed "Subject B". At the Crane house, Gerald once again injected himself with the inoculation serum and suffered from the hallucination of his wife in a burning fire. Afterward, he informed Jonathan that it was almost his turn to be cured of fear, as it was working.
Penguin starts his remodeling of the nightclub, and elsewhere Fish questions Mace as to why he was the leader of the underground prison, as there were a lot of tough guys around. Later Penguin arrives at the GCPD to bring Detective Gordon and invitation to the grand re-opening of the nightclub, but he has an awkward encounter with Edward Nygma who attempted to give him a riddle to answer though he was dismissed. When Jim arrived, he turned down Oswald's offer of attending the nightclub and though Penguin offered to help him with his case, Gordon rejected the offer telling him he didn't want him coming to the GCPD again. Offended, Penguin tells Jim that he shouldn't treat him that way, and that he'd one day soon he'd need his help. At the Crane house, Gerald injected Jonathan with the serum. During his journey, Bruce comes across a pile of rocks with his and his father's initials on them, from years previous. In a fit of rage, he knocks the pile over and begins throwing them everywhere in a fit of rage. He then sinks to his knees crying, and soon after due to an oversight, he falls down a steep slope, badly spraining his ankle. At the GCPD, Jim draws a line with Lee regarding PDA during the job, though the two are interrupted by Bullock.
At Falcone Manor, Maroni visits Falcone to address the issue of Penguin. Despite wanting revenge against him, he decides to leave him alive after Falcone gives shows him Judge Stanley Turnball who Falcone had abducted when he had been out with a younger man. Having the Judge whipped, while his torturer took pictures, much to Maroni's amusement. At the GCPD, Gordon and Bullock discover that Crane's real fear he had been generated by the guilt of not being able to save his wife from a fire that had occurred in their house, years ago. With that information, they decide to visit the old Crane house. At the Crane house, Jonathan tries to escape from his father, as to not have to continue to be subjected to the injections but only manages to get so far, by an old scarecrow, and in the end, Gerald manages to convince him to return since their work was for the good of humanity.
Looking out into the darkness, Alfred decides to go look for Bruce, while Bruce with sprained ankle, continued to try climbing the slope. Meanwhile in the underground prison Fish uses her wits to bypass the security of Mace and finally get close enough to take his knife from him, assassinating him and taking his place as the head of the prison. Gordon and Bullock arrived at the old house Crane house, where, Gerald and Jonathan attempted to escape through the courtyard. Stopping at the hay under the Scarecrow, Gerald decided to conclude the injections and administered a large dose to Jonathan that him convulsing wildly before in fear of the Scarecrow. Fearing nothing, Gerald takes his gun and shoots at the Detective, though they quickly shoot him down. Finding Jonathan convulsing, Gordon quickly tells Bullock to call an ambulance. Meanwhile, after an hour crawling to reach the top of the hill, Bruce finds Alfred located next to a campfire with food and drink. Alfred then helped Bruce up, and Alfred suggests that they wait and watch the sunrise like Bruce did with his father. Bruce agrees, though only if Alfred can handle it, and afterward, is offered tea by Alfred.
At his nightclub, Penguin is visited by Don Maroni, much to his surprise, there the Don makes his intentions clear to not hurt Penguin, due to a deal he made with Falcone. However he warns him that the second Falcone was out of the picture, so was he. The next day Alfred and Bruce watch the sunrise together. At the GCPD, Leslie invites him to the circus, and Jim once again reminds Leslie of no PDA in front of their peers, and surprisingly she accepts his terms. At the underground prison Fish announces to her fellow prisoners that there'd be order from then on, though soon after their captors entered bringing in a woman whose eyes had been removed, to everyone's horror. Back in Gotham City, Jim visits the hospital to check on the state of Jonathan Crane. There, Doctor Anderson informs him that the injections had altered Crane's brain activity, leaving him in a constant state of terror. In the room, Jonathan began to experience a horrific hallucination of a giant scarecrow coming towards him, causing Jonathan to scream in terror.