Jim Gordon and Bruce Wayne face the chaos Gotham City has become, as the villains who survived the attack on the city begin to resurface and claim various territories; Selina Kyle grapples with how to deal with her uncertain future.
Gordon and Bullock investigate a location where several kids have been kidnapped; Barbara proves to be an unlikely ally to Gordon; Bruce looks into an alleged witch with healing powers for Selina; Nygma deals with his demons.
With the creation of Haven as a safe place for refugees, Gordon hopes to stop the gang-fighting in Gotham. Selina is determined to find Jeremiah and convinces Bruce to help her. Meanwhile, Penguin goes to Haven to reclaim his staff.
Gordon and Penguin are forced to work together and alliances are shaken when Lucius, Nygma and Barbara all have different ideas of the culprit behind recent events at Haven. Meanwhile, Selina continues her quest for revenge against Jeremiah.
A military task force, led by Eduardo Dorrance is called in to provide relief to Gotham. Meanwhile, Nygma looks for answers from Penguin, who leads him back to Hugo Strange. Then, Bruce is concerned about Selina's recent behavior.
Gordon assembles an unlikely team to protect Gotham from Eduardo Dorrance and his Delta Force. Just as Lee Thompkins resurfaces, Barbara reveals shocking news that will change Gordon's life forever. Meanwhile, Selina and Penguin team up to outsmart fellow villain Magpie.
Gordon races to uncover the criminal element threatening to end talks of Gotham's reunification with the mainland. A very much alive Jeremiah returns and organizes a twisted recreation of the hug of Bruce's parents with the help of Jervis Tetch aka Mad Hatter.
Bullock's past comes back to haunt him when he and Gordon investigate two murders at Sirens. Meanwhile, Bruce and Alfred explore the tunnels beneath the city, and Penguin and Nygma's plans to escape are thwarted by the least likely of suspects.
After Gordon is shot in an attempt to establish a cease-fire, he hallucinates a trial for his life that could have deadly real consequences. Meanwhile, Ivy returns and puts her spell on Bruce, leaving Selina to defend herself. Lee has a life-changing moment as Barbara and Penguin consider their next moves.
On the precipice of Gotham's reunification, Gordon and Bruce find themselves face-to-face with a newly transformed Eduardo, and discover the real mastermind behind the city's current chaos. Meanwhile, a pregnant Barbara turns to Lee for help.
As Bane enacts his final plan for Gotham's destruction, Gordon rallies his former enemies to save the city. Meanwhile, Nyssa al Ghul kidnaps Barbara's newborn daughter, with ambitions to raise her as her own. Then, Bruce's decision to leave Gotham points him to his destiny, while devastating Selina.
The series flash-forwards 10 years into the future, as Bruce is set to return to Gotham for the opening of the new Wayne Tower. A series of crimes leads Gordon to believe Penguin and The Riddler are up to their old tricks. However, when Bullock is framed for a hug, Gordon begins to piece together an even more sinister plot targeting the city, and a new figure emerges from the shadows to be the hero Gotham desperately needs.