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.
With the deadly virus spreading throughout the city, the search for the antidote continues, as Fish Mooney, The Riddler and Penguin reveal plans of their own. Bruce meets Ra's Al Ghul and completes his last task in order to fulfill his destiny, but realizes he can't let go of his past.
As the third season concludes, Gordon tries to win back Lee, and past alliances within Gotham City are broken, while new alliances are formed.