After Bridgit Pike is kidnapped by her brothers, a new spark of courage ignites within her, as she chooses to take control of her future. Meanwhile, Kringle and Nygma's relationship will take a new step and Penguin and Galavan continue to battle for control of Gotham City's underworld.
Alfred and Selina help Bruce on his quest to find his parents' killer Matches Malone. Meanwhile, Gordon follows up with Edward Nygma on Kristin Kringle's whereabouts. Hugo Strange continues his treatment to reduce Penguin's aggression.
Gordon and Bullock investigate a trail of clues left in a museum robbery which unbeknownst to them were left by Nygma in a dangerous game of cat and mouse. Gordon's past comes back to haunt him when an anonymous person threatens to expose his hand in Galavan's murder. Meanwhile Penguin's visit to some old friends leads him to meet his father Elijah Van Dahl (Paul Reubens). and Bruce practices his street smarts.
After Gordon is removed from protective custody, he begins to face new threats and dangers inside prison walls. In order to survive he must rely on a new friend as well as Bullock and other outside help. Meanwhile, Penguin grows closer to his Father, while his step-mother and step-siblings move forward with their own plans for the family.
In an attempt to clear his name, Gordon steals his case file and approaches Nygma for help. Meanwhile, Penguin discovers his step-family's role in his father's death, and awakens from his conditioning.
Hugo Strange welcomes a familiar face to Gotham after he resurrects Fish Mooney in Indian Hill. Meanwhile, Bruce discovers a friend is in danger and teams up with Gordon, Alfred and Lucius while uncovering more of his experiments.