A new recruit in Captain Sarah Essen's Gotham City Police Department, Detective James Gordon is paired with Harvey Bullock to solve one of Gotham's highest-profile cases: the murder of Thomas and Martha Wayne. During his investigation, Gordon meets the Waynes' son Bruce, now in the care of his butler Alfred Pennyworth, which further compels Gordon to catch the mysterious killer. Along the way, Gordon must confront mobstress Fish Mooney, mafia led by Carmine Falcone, as well as many of Gotham's future villains such as Selina Kyle, Edward Nygma, and Oswald Cobblepot. Eventually, Gordon is forced to form an unlikely friendship with Wayne, one that will help shape the boy's future in his destiny of becoming a crusader.
Detective James Gordon performs his work in the dangerously corrupt city of Gotham, which consistently teeters between good and evil.
Detectives Gordon and Bullock investigate a child trafficking ring preying on Gotham's street kids, including Selina Kyle. Penguin resurfaces in the countryside and begins to make his way back to Gotham.
Gordon and Bullock track down a vigilante who uses weather balloons to kill corrupt citizens; Cobblepot gets a job close to a major figure in the underworld.
Politicians on both sides of the Arkham district issue are in danger as the vote approaches; Gordon gets a visit from an old friend.
Gordon and Bullock search for the source of a new street drug that causes euphoria then death. Oswald Cobblepot works his way deeper into Maroni's inner circle. Fish Mooney continues to plot against Falcone.
When a killer begins targeting the first born of Gotham's elite, Bullock is forced to confront traumatic memories from a nearly identical case he worked in the past. Gordon is confronted by past decisions.
As violence between Maroni and Falcone continues to escalate, Penguin reveals a new element of his manipulative strategy, forcing Gordon to deal with the consequences of his decision to spare Penguin’s life.
Gordon and Bullock investigate a Gothamite who runs a deadly fight club for candidates applying for a job at his financial firm. Meanwhile, Bruce returns to school and gets a visit from a new friend.
Trying to close the Wayne murder case, a young Harvey Dent and Gordon team up, much to Mayor James’ chagrin. Meanwhile, Penguin makes contact with Mooney’s secret weapon, Liza.
Selina leads a new friend on a perilous journey through Gotham to evade the assassins who are on her trail. Following a misstep, Gordon is reassigned to duty at Arkham Asylum.
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.
In an attempt to get his job back, Gordon seeks to capture Jack Gruber, a deranged electrical genius who escapes Arkham Asylum. Meanwhile, Falcone struggles to hold onto his empire after Fish Mooney makes her next move.
When the key witness in a homicide ends up dead while being held for questioning by the police, Gordon suspects that it’s an inside job and looks to an old friend for information. Meanwhile, Oswald Cobblepot takes control of one of Fish Mooney’s prized possessions, as she gets a small taste of her own medicine.
Fish Mooney reveals a secret of Oswald Cobblepot's, prompting Maroni to take him on a trip to test his loyalty. Meanwhile, Gordon and Bullock hunt down a killer who targets victims with severe phobias and Bruce Wayne confronts Gordon for failing to make progress on his parents' murder case.
Gordon and Bullock set out to stop Gerald Crane, a biology teacher who has been harvesting the 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.
Gordon takes Dr. Leslie Thompkins to the circus, but the day turns quickly when the circus comes under attack. Then, Falcone enlists Butch Gilzean to help Penguin with the night club, while Fish Mooney is otherwise occupied. Also, Bruce Wayne schedules a meeting with the Wayne Enterprises board.
Following several bank robberies, Gordon and Bullock investigate the Red Hood gang. Selina Kyle continues to bond with Barbara, and Fish Mooney tries to reclaim her position in the underworld.
While Gordon seeks information about the recent controversy with Commissioner Loeb, Fish’s allegiance with the prisoners is questioned when she appears to join forces with Dr. Dulmacher. Meanwhile, after an attack close to home, Bruce deals with the aftermath.
Gordon and Bullock inspect a cold case involving the Ogre, a serial killer who targets young women in Gotham City. Meanwhile, Fish plots her escape from the Dollmaker, and Bruce and Selina confront Reggie.
Gordon and Bullock continue their investigation of the Ogre, who begins to make his move on someone close to Gordon. Meanwhile, Bruce and Selina team up to expose a corrupt Wayne Enterprises employee and Nygma comes to Kristin Kringle’s defense.
The Ogre breaks down Barbara’s emotions, while Gordon and Bullock go to great lengths to track him down. Meanwhile, Penguin leads a massacre, beginning an epic war, while Bruce learns the truth about Wayne Enterprises and Nygma deals with his recent actions.
As Gotham City’s gang war reaches its boiling point, Fish Mooney goes head-to-head with Maroni and Penguin in an attempt to re-stake her claim on the city. Meanwhile, Barbara and Leslie Thompkins are brought together after recent events, and Bruce searches Wayne Manor for any hints that his father might have left behind.