Penguin is King of Gotham and after a shakeup at the GCPD, Detective James Gordon's moral compass wavers, as he seeks help from Penguin. Meanwhile, Bruce Wayne continues to explore the secrets from his father's office, and Gotham newcomers Theo Galavan and his sister, Tabitha, make friends with some unlikely allies - a group of dangerous inmates from Arkham.

Gordon and Bullock track down a nemesis from the past, leading to a standoff between Jerome and Gordon. Meanwhile, a magic show at the Gotham Children's Hospital gala turns into a hostage situation.

Galavan and Penguin join forces with a dangerous family in Gotham. Then, as the rivalry between the Waynes and the Galavans resurfaces, Gordon struggles to maintain order in the city.

Butch leads Penguin and his men to the warehouse where Gertrude is being held, as Penguin plots his revenge on Galavan for kidnapping his mother. Meanwhile, Nygma deals with the aftermath of a deadly accident.

Gordon and Barnes continue cleaning up Gotham, and Gordon comes face-to-face with one of the city's most dangerous hitmen, Eduardo Flamingo. Meanwhile, Nygma and Penguin cross paths again, and Bruce pressures Galavan into handing over the name of his parents' murderer.

When Bruce Wayne is kidnapped, Gordon must look to some unlikely and dangerous allies for help. It is a battle of the villains, and not everyone makes it out alive.

While Gordon, Bruce and Lucius remain at Indian Hill, the city of Gotham will be met with a new threat as Hugo Strange’s inmates devise a plan to escape and start their new lives in Gotham.