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.

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.

Gordon and Bullock sift through evidence from the murder at Lee and Mario's engagement party; Ivy discloses her identity to Selina and Bruce.

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.

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 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.

Gordon races against the clock to save the city from the Alice Tetch Virus, when Lee Thompkins intercepts with a plan of her own. Also, Alfred sees a big change in Bruce Wayne after his work with The Shaman. 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. Meanwhile, Gordon tries to win back Lee, and past alliances within Gotham City are broken, while new alliances are formed.

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.