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.
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.
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.
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 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.
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 into Gotham city.
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.
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.
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 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.
Nygma comes face-to-face with Butch Gilzean, but he is not who he used to be. In an attempt to regain power and identity, Nygma decides to put his former partner's skills to the test. Meanwhile, Sofia Falcone takes action to protect her own life by appealing to Penguin's vulnerable side. With the power of the dagger in his possession, Bruce surprises those around him with his bold actions.
With Professor Pyg striking fear throughout Gotham, Gordon and Bullock head into the Narrows to look for clues. Bruce Wayne meets a former friend, Grace, who convinces him to come along for a night out with some old classmates. Meanwhile, Sofia's relationships with Penguin and Gordon continue to evolve.
Professor Pyg continues to torment Gotham city, involving Jim Gordon whenever possible. Sofia and Penguin get ready for a fundraiser for the orphanage, and things don't go as planned when Professor Pyg shows up as the chef. Meanwhile, Bruce's partying gets in the way of his relationship with Alfred.
Things get complicated for Gordon, Sophia and Penguin when Carmine Falcone comes to town. Alfred tries to get through to Bruce once and for all, while Nygma struggles to gain control over The Riddler persona and Tabitha attempts to make Grundy remember his past. Meanwhile, a familiar smile resurfaces in Gotham.
Jeremiah warns a skeptical Gordon of more destruction coming Gotham's way, and Gordon is forced to make a potentially devastating decision. Meanwhile, Barbara rallies together a team to secure her position, as alliances in the underworld shift and prove no one can be trusted. Then, Bruce is forced to come to terms with the future.
Jim Gordon and Bruce Wayne face the chaos Gotham City has become. Their mission to keep the city safe becomes more complicated, as the villains who survived the attack on the city begin to resurface and claim various territories. Meanwhile, Selina Kyle grapples with how to deal with her uncertain future.
After Gordon is shot in an attempt to establish a cease-fire, he hallucinates a trial for his life that could have deadly real consequences. Meanwhile, Ivy returns and puts her spell on Bruce, leaving Selina to defend herself. Lee has a life-changing moment as Barbara and Penguin consider their next move.
As Bane enacts his final plan for Gotham’s destruction, Gordon rallies his former enemies to save the city. Meanwhile, Nyssa al Ghul kidnaps Barbara’s newborn daughter, with ambitions to raise her as her own. Then, Bruce’s decision to leave Gotham points him to his destiny, while devastating Selina.
The series flash-forwards 10 years into the future, as Bruce is set to return to Gotham for the opening of the new Wayne Tower. A series of crimes leads Gordon to believe Penguin and The Riddler are up to their old tricks. However, when Bullock is framed for a murder, Gordon begins to piece together an even more sinister plot targeting the city, and a new figure emerges from the shadows to be the hero Gotham desperately needs.