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.

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.

After Gordon is removed from protective custody, he begin's to face new threat's and danger's inside prison wall's in order to survive he must rely on a new friend as well as Bullock and other outside help. Meanwhile, Penguin grow's closer to his Father, while his step-mother and step-siblings move forward with their own plan's for the family.

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.

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.

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.

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. Meanwhile, Gordon tries to win back Lee, and past alliances within Gotham City are broken, while new alliances are formed.

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 is called to the scene after The Toy Maker is hired to assassinate one of Gotham's doctors. Lee Thompkins begins to try to rebuild the Narrows, with Nygma as her partner. Meanwhile, Alfred's new life in the Narrows becomes quite complicated. Ivy reveals her new persona to Selina, with some sinister plans in mind.

The Arkham inmates are still running freely in Gotham and they're only getting more difficult to catch. Gordon develops a plan, but reluctantly has to turn to Bruce for help. Meanwhile, Barbara finds out just how far her new friends are willing to go for her.

Gordon and Bullock investigate a location where several kids have been kidnapped. Barbara proves to be an unlikely ally to Gordon. Bruce looks into an alleged witch with healing powers for Selina. Nygma deals with demons of his own.