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.

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.

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, with Sofia Falcone in town, she is on a mission to win back Gotham from Penguin.

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.

Ivy tracks a secret project on which Wayne Enterprises is working and begins to target anyone that can give her information. Meanwhile, Jerome becomes obsessed with Penguin in Arkham. Also, Gordon begins to second guess his deal with Sofia and an unsettling dream sequence shakes up Bruce.

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 figure out who the clever thief is behind the robberies of various bank branches in Gotham. Meanwhile, Barbara is put in danger, forcing Tabitha to recruit help.

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.

Jeremiah warns a skeptical Gordon of more destruction coming Gotham's way, and Gordon is forced to make a potentially devastating decision. Meanwhile, Barbara rallies together a team to secure her position, as alliances in the underworld shift and prove no one can be trusted. Then, Bruce is forced to come to terms with the future.