Things get complicated for Gordon, Sophia and Penguin when Carmine Falcone comes to town. Alfred tries to get through to Bruce once and for all; Nygma struggles to gain control over the Riddler persona; and Tabitha attempts to make Grundy remember his past. Meanwhile, a familiar smile resurfaces in Gotham.
Professor Pyg continues to torment Gotham city, involving Jim Gordon whenever possible. Sofia and Penguin get ready for a fundraiser for the orphanage, and things don't go as planned when Professor Pyg shows up as the chef. Meanwhile, Bruce's partying gets in the way of his relationship with Alfred.
Grundy and Nygma become main attractions at Cherry's Place in the Narrows; Penguin wants revenge when he hears Nygma is mocking him on stage and enlists the Sirens for help; and Gordon is offered the position of GCPD captain, putting him at odds with Bullock.
With Professor Pyg striking fear throughout Gotham, Gordon and Bullock head into the Narrows to look for clues. Bruce Wayne meets a former friend, Grace, who convinces him to come along for a night out with some old classmates. Meanwhile, Sofia's relationships with Penguin and Gordon continue to evolve.
Gordon and Bullock are hot on a serial killer who has been assassinating cops and dressing his victims in the severed heads of pigs as his signature mark. Meanwhile, Sofia tries to win over Penguin, and Thompkins, Nygma and Grundy find themselves an unlikely home at Cherry's place.
Nygma comes face-to-face with Butch Gilzean, but he is not who he used to be. In an attempt to regain power and identity, Nygma decides to put his former partner's skills to the test. Meanwhile, Sofia Falcone takes action to protect her own life by appealing to Penguin's vulnerable side. With the power of the dagger in his possession, Bruce surprises those around him with his bold actions.
Bruce Wayne puts the lives of Gotham Natural History Museum historian Niles Winthrop and his grandson, Alex, in danger in an attempt to uncover the meaning behind his prized knife from the auction. Meanwhile, Ra's Al Ghul proves he'll take deadly measures to achieve what he wants. Also, Sofia Falcone is on a mission to win back Gotham from Penguin.
Gordon takes matters into his own hands when he travels to Miami in attempts to persuade Carmine Falcone for his help in the fight against Penguin. There, he meets Carmine's daughter, Sofia, who unexpectedly follows Gordon back to Gotham. The battle for Penguin's prized weaponry continues during auction night at the Iceberg Lounge and Bruce's presence puts him on Penguin's radar.
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.
In the Season 4 premiere, 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; and, in the aftermath of his encounter with Ra's Al Ghul, Bruce begins his vigilante watch.