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.
While Gordon, Bruce and Lucius remain at Indian Hill, the city of GOTHAM will be met with a new threat as Hugo Strange's inmates devise a plan to escape and start their new lives.