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 doppelganger 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.

The effects of a recent incident begin to cause Barnes to go mad; Nygma is over his head in his relationship with Isabella; Carmine Falcone throws an engagement party for Lee and Mario.

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.

Gordon tracks down the weapon the Court of Owls intend to use for the destruction of Gotham; Kathryn and Temple Shaman tell Bruce about their next move; Ivy offers Selina help.

Temple Shaman takes Bruce to the next phase of his training; Gordon and Bullock discover a crystal owl that carries the biggest secrets of Gotham's underworld; Nygma and Penguin must work together to get out of a tricky situation.

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.

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.

Arkham's "finest" give Gordon and Bullock a run for their money, as they hatch a plan to escape the asylum. Meanwhile, Bruce devises his own strategy to thwart their plans. Also, Barbara gets an offer she can't refuse.

Gordon and Bullock try to stay one step ahead as Jerome zeros in on his next target. Meanwhile, Nygma hosts a riddle game show in the Narrows and faces his toughest challenger in Lee Thompkins, and Penguin goes to see Butch with a proposal.

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 races to uncover the criminal element threatening to end talks of Gotham's reunification with the mainland. A very much alive Jeremiah returns and organizes a twisted recreation of the murder of Bruce's parents with the help of Jervis Tetch aka Mad Hatter.