Penguin is King of Gotham and after a shakeup at the GCPD, Detective James Gordon's moral compass wavers, as he seeks help from Penguin. Meanwhile, Bruce Wayne continues to explore the secrets from his father's office, and Gotham newcomers Theo Galavan and his sister, Tabitha, make friends with some unlikely allies - a group of dangerous inmates from Arkham.
On the heels of his reinstatement, Gordon is thrust onto the high-profile case tracking the deadly inmate escape from Arkham Asylum. Meanwhile, Galavan plans his next move, while Bruce asks for help from his fathe's old friend to unlock the secrets in his office, and Nygma asks out Kristin Kringle on a date.
Gordon and Bullock track down a nemesis from the past, leading to a standoff between Jerome and Gordon. Meanwhile, a magic show at the Gotham Children's Hospital gala turns into a hostage situation.
Captain Barnes is called to duty to create a law-abiding task force, with the help of Gordon. Meanwhile, Penguin gets caught up in a favor for Galavan, and Nygma asks Kringle out on a date.
Galavan and Penguin join forces with a dangerous family in Gotham. Then, as the rivalry between the Waynes and the Galavans resurfaces, Gordon struggles to maintain order in the city.
After Bridgit Pike rejoins her brothers, a new spark of courage ignites within her, as she chooses to take control of her future. Meanwhile, Kringle and Nygma's relationship will take a new step and Penguin and Galavan continue to battle for control of Gotham City's underworld.
Butch leads Penguin and his men to the warehouse where Gertrude is being held, as Penguin plots his revenge on Galavan for kidnapping his mother. Meanwhile, Nygma deals with the aftermath of a deadly accident.
Galavan sends Barbara after Jim Gordon, while he tries to make a business deal with Bruce Wayne. Barnes and Bullock are hot on Barbara's trail, and Nygma has a run-in with a familiar face.
Gordon and Barnes continue cleaning up Gotham, and Gordon comes face-to-face with one of the city's most dangerous hitmen, Eduardo Flamingo. Meanwhile, Nygma and Penguin cross paths again, and Bruce pressures Galavan into handing over the name of his parents' murderer.
Gordon confronts a suspect who is connected to Galavan, but falls short of obtaining any information. Meanwhile, Bruce gets one step closer to discovering the name of his parent's killer.
When Bruce Wayne is kidnapped, Gordon must look to some unlikely and dangerous allies for help. It is a battle of the villains, and not everyone makes it out alive.
Penguin takes a hit for Galavan's murder, but doesn't let Gordon off easily. Meanwhile, Gordon and Bullock investigate the body-snatching spree of Victor Fries, one of Gotham's preeminent cryogenics engineers.
As Gordon, Bullock and Barnes continue the search for Victor Fries, they are forced to look to his wife, Nora, for help. Meanwhile, Penguin is introduced to Hugo Strange, and Alfred reveals some crucial information to Bruce about his parents' murderer.
Alfred and Selina help Bruce on his quest to find his parents' killer, Matches Malone. Meanwhile, Gordon follows up with Edward Nygma on Kristen Kringle's whereabouts and Hugo Strange continues his treatment to reduce Penguin's aggression.
Gordon and Bullock investigate a trail of clues left in a museum robbery, which, unbeknownst to them, were left by Nygma in a dangerous game of cat-and-mouse. Meanwhile, Gordon's past comes back to haunt him when an anonymous person threatens to expose his hand in Galavan's murder. Also, Penguin's visit to some old friends leads him to meet his father, Elijah Van Dalh, and Bruce practices his street smarts.
After Gordon is removed from protective custody, he begins to face new threats and dangers inside prison walls. In order to survive, he must rely on a new friend, as well as Bullock and other outside help. Meanwhile, Penguin grows closer to his father, while his step-mother and step-siblings move forward with their own plans for the family.
In an attempt to clear his name, Gordon steals his case file and approaches Nygma for help. Meanwhile, Penguin discovers his step-family's role in his father's death, and awakens from his conditioning.
After leaving Arkham Asylum, Barbara attempts to make amends with Gordon. Then, Bruce and Alfred track down one of Thomas Wayne's former friends from Project Chimera, but Hugo Strange disrupts their plans.
Gordon and Bruce question Professor Strange about Project Chimera, which leads Strange to send the newly resurrected Galavan to confront Gordon. Meanwhile, Nygma investigates who Professor Strange is.
Azrael is on the loose in Gotham City, which sparks Penguin's need for revenge. Meanwhile, Bruce enlists the help of Selina Kyle to help track down Professor Strange, as he evades arrest for his experiments.
Hugo Strange welcomes a familiar face to Gotham after he resurrects Fish Mooney in Indian Hill. Later, Bruce discovers a friend is in danger and teams up with Gordon, Alfred and Lucius, while uncovering more of Strange's experiments.
Gordon fears Jonathan Crane is still alive and back in Gotham, when The Scarecrow's signature MO is used in a series of robberies. Meanwhile, Penguin's "licensing" of crime in the city backfires during the grand opening of his new Iceberg Lounge. Also, in the aftermath of his encounter with Ra's Al Ghul, Bruce begins his vigilante watch.
Under pressure to prove that the GCPD is still powerful, Gordon attempts to bring in Jonathan Crane. However, Gordon puts himself in a dangerous situation at Arkham when he is forced to fight off lunatics and the demon within himself. Meanwhile, with Barbara's unexpected return, Selina and Tabitha must consider risks that come with joining her in the weapon business.
Gordon takes matters into his own hands when he travels to Miami in attempts to persuade Carmine Falcone for his help in the fight against Penguin. There, he meets Carmine's daughter, Sofia, who unexpectedly follows Gordon back to Gotham. The battle for Penguin's prized weaponry continues during auction night at the Iceberg Lounge and Bruce's presence puts him on Penguin's radar.
Bruce Wayne puts the lives of Gotham Natural History Museum historian Niles Winthrop and his grandson, Alex, in danger in an attempt to uncover the meaning behind his prized knife from the auction. Meanwhile, Ra's Al Ghul proves he'll take deadly measures to achieve what he wants. Also, with Sofia Falcone in town, she is on a mission to win back Gotham from Penguin
Gordon works in a monster-ridden Gotham as a bounty hunter and seeks to find answers about the Indian Hill escapees, and why their powers appear to be killing them. Meanwhile, Bruce’s doppelganger roams the streets, and Barbara and Tabitha open a new nightclub called The Sirens.
Fish Mooney takes matters into her own hands to locate Hugo Strange, forcing Gordon to reluctantly team up with journalist Valerie Vale to find her. Penguin rises in popularity after criticizing the work of the GCPD and Bruce's investigation of the Court of Owls is compromised. Meanwhile, Ivy Pepper is reintroduced into Gotham city.
Hypnotist Jervis Tetch/Mad Hatter arrives in Gotham to search for his sister, Alice, and hires Gordon to help find her. Meanwhile, Penguin decides to run for mayor and Bruce's doppelganger begins to channel him, causing some confusion around town.
Penguin gains power as he narrows in on the nomination for Mayor of Gotham. Meanwhile, Gordon turns Alice into the GCPD for the bounty. Also, Bruce and Alfred race to find Bruce’s doppleganger after learning he’s assumed Bruce’s identity.
Crime in Gotham is at an all-time high, as Penguin struggles to uphold his promises to the city. Meanwhile, Butch goes down a dark path with the infamous Red Hood Gang and Bruce begins to investigate Ivy's whereabouts.
Mad Hatter sets his eyes on his next victims, forcing Jim Gordon to make some tough decisions. Meanwhile, Penguin and Nygma's relationship evolves, and a familiar face comes back into Nygma's life.
After coming in contact with a substance by the hand of Mad Hatter, Jim Gordon gets led on a psychedelic trip and must confront his past, present and future. Meanwhile, Penguin struggles with Nygma's new relationship.
Barnes begins to feel the effects of a recent incident and begins to go mad. Meanwhile, Nygma is out of his depth in his relationship with Isabella and Carmine Falcone throws Lee and Mario an engagement party.
Gordon and Bullock become suspicious of Barnes, and comb through evidence of the murder at Lee and Mario’s engagement party. Nygma goes to Penguin when he hasn’t heard from Isabella. Meanwhile, Ivy reveals her identity to Selina and Bruce, but quickly leads them to trouble.
On the eve of their rehearsal dinner, a threat to Mario and Lee is exposed, and Falcone looks to Jim for help. Meanwhile, Nygma seeks revenge and Bruce learns more about The Court of Owls.
As the virus begins to spread in Gotham, the laboratory that is developing a cure is compromised. Mario and Gordon face off before the wedding, Selina meets an unexpected face and Barbara comes to Nygma with information about Isabella.
Falcone places a hit on Gordon after learning that he shot Mario. Gordon and Bullock discover a follower of Jerome, who plans to bring him back to life. Meanwhile, Penguin spirals out of control before the biggest television interview of his Mayoral career, and Bruce and Selina deal with Selina's mom's return to Gotham.
On the run from Gordon and Bullock, Dwight tries to revive Jerome and, in turn, activates his acolytes around Gotham City. Meanwhile, Selina's mom's intentions in Gotham are revealed, and the power play between Penguin and Nygma escalates as Barbara's plans are set in place.
With Jerome on the loose with one target in mind, Bruce and Alfred's safety is compromised. Meanwhile, Gordon's uncle Frank pays him a visit, and Nygma and Penguin are forced to confront their issues face-to-face, with possible deadly consequences.
Nygma convinces himself that he doesn't need Penguin to succeed and begins to introduce himself to Gotham as "The Riddler." Bullock and Lucius Fox get caught up in Nygma's mind games, while Gordon learns troubling news about his father's death. Meanwhile, the Court of the Owls reveals its next move.
The Court of Owls devises a new plan regarding the future of Gotham, as Gordon uncovers information about his father and uncle's past, connecting him back to the organization. Meanwhile, Bruce wakes up in the temple and learns of the Shaman's wish for him.
Some of Gotham's most unhinged villains band together, while The Riddler continues his conquest of the city. Gordon is on a search for answers and all roads keep leading him back to the Court of Owls. Meanwhile, as Alfred begins to notice a change in Bruce, Bruce 2 confides in Selina.
Gordon discovers the weapon the Court of Owls will use to destroy Gotham, which leads him on a dangerous path as he tracks it down. Meanwhile, Kathryn and Temple Shaman reveal their next move to Bruce, and Ivy comes to Selina's aid
Temple Shaman reveals his hand to Bruce Wayne and sets up the next phase of training. Gordon and Bullock are put into danger as they come across a crystal owl that reveals the most coveted secrets of Gotham's underworld. Meanwhile, Nygma and Penguin are forced to work together to get out of a tricky situation.
Gordon races against the clock to save the city from the Alice Tetch virus, when Lee Thompkins (Morena Baccarin) intercepts with a plan of her own. Also, Alfred sees a big change in Bruce Wayne after his work with The Shaman (guest star Raymond J. Barry). Meanwhile, some of Gotham's most deranged villains band together.
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.
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.
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.
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.
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.