Jim Gordon and Bruce Wayne face the chaos Gotham City has become, as 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.

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 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 murder 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.

Bruce returns to Gotham for the opening of the new Wayne Tower; when Bullock is framed for a murder, Gordon begins to piece together a sinister plot targeting the city; a new figure emerges to be the hero Gotham needs.