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.
With Professor Pyg striking fear throughout Gotham, Gordon and Bullock head into the Narrows to look for clues. Bruce Wayne meets a former friend, who convinces him to come along for a night with some old classmates.
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. Meanwhile, Gordon is offered the position of GCPD Captain.
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.
Gordon tries to broker a deal with Penguin that involves Sofia. Meanwhile, Alfred tries to pull Bruce out of his teenage-angst and downward spiral, as Lee Thompkins gains more control over the Narrows.
Carmine Falcone comes to town, making things complicated for Gordon, Sophia and Penguin. Alfred tries to get through to Bruce once and for all, Nygma struggles to gain control over the Riddle persona, and Tabitha attempts to make Grundy remember his past. Meanwhile, a familiar smile resurfaces in Gotham.
Gordon is called to the scene when the Toy Maker is hired to assassinate a doctor in Gotham; Lee tries to rebuild the Narrows with Nygma's help; Alfred's new life becomes complicated; Ivy shows Selina her new persona.
Ivy picks her next target, leading Gordon and Lucius back to an old friend, as Selina tries to take matters into her own hands. Sofia wants full control of Gotham and turns to Lee about the state of the Narrows. Meanwhile, Bruce tries to make amends with Alfred, and Nygma visits Arkham.
Bullock and Gordon try to track down someone who is key in Sofia's control over Gotham. Meanwhile, Penguin, Lee and Nygma enlist an unlikely ally as they seek revenge, and Selina asks Bruce for a favor to help rid her of her guilt over Ivy.
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 (guest star Cameron Monaghan 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.
As Gotham falls into complete anarchy, a team of unlikely heroes step up to save it. Bullock takes the lead at the GCPD and Bruce's psychological limits are tested as those close to him are put in danger.