While Bruce continues to try and penetrate his father's vault, Loeb fires Jim from the force... and Jim takes extreme measures to get reinstated. Meanwhile, Barbara settles in to life at Arkham Asylum and makes several new friends.
Theo sends his team of Maniax out on a new assignment, but it's only the prelude to something much larger and bloodier. Meanwhile, Alfred tries to protect Bruce, and turns to Lucius Fox for help.
Jim is reluctant to turn to Oswald for help, so Harvey pays the new crime boss a visit. Meanwhile, Jerome poses as a magician to infiltrate a children's hospital benefit, but discovers that Theo has other plans in store for him.
The GCPD gets a new captain and he immediately cleans house and brings on Jim as his second-in-command... unaware of Jim's background with the Penguin. Meanwhile, Theo asks the Penguin for a favor, and Bruce and Theo have lunch.
Theo forces Oswald to hire the Pike Brothers to torch select buildings in Gotham, and the Pikes use their sister Bridgit. Meanwhile, Theo asks Jim for his endorsement, Oswald orders Butch to lend a hand, and Leslie invites Edward and Kristen over for fondue.
Jim promises Selina to keep the new Firefly safe, but discovers that the girl doesn't want to turn herself in. Meanwhile, Theo and Silver invite Bruce to dinner, Edward tells Kirsten the truth, and Butch finds out where Gertrude is imprisoned.
Jim begins to realize that Theo has orchestrated everything to become mayor. Meanwhile, Oswald swears revenge on the man who killed his mother, and Edward tries to cover up Kristen's death but faces an opponent that knows his every move.
While Theo tries to convince Bruce to sign over Wayne Enterprises to him, he sends Barbara as a distraction to keep Jim occupied. Meanwhile, Edward has one last picnic lunch with Kirsten before disposing of her body, and ends up meeting a familiar figure.
While Jim and Barnes takes on hit men sent to kill Jim, Edward convinces Oswald that he has something to live for in Gotham. Meanwhile, Alfred forbids Bruce from seeing Silver again, even though she may hold the key to finding out whose his parents' killer was.
While Jim and Harvey try to track down the elusive monks performing blood sacrifices, Bruce proposes a new deal with Silver to find out the name of his parents' killers. Meanwhile, Edward gets used to having a roommate.
Jim discovers that the Order of Dumas is prepared to sacrifice Bruce at midnight, and turns to Oswald for help. Meanwhile, Leslie gives Jim startling news, Tabitha comes to a decision about her brother, and a new vigilante stalks the streets of Gotham.
A new killer stalks the streets of Gotham, freezing victims with liquid helium for his experiments in cyrogenic reanimation. Meanwhile, Jim goes before the board for his actions in taking down Theo, and a captured Oswald is sentenced to Arkham.
The GCPD take Nora to Arkham when her condition worsens, and Victor breaks into the asylum in his new guise as Mr. Freeze. Meanwhile, Oswald undergoes extreme treatment at Hugo's hands, and Alfred finds the mysterious M. Malone that killed Bruce's parents.
While Hugo continues Oswald's treatment at Arkham, Bruce goes on a hunt for his parents' killer.
Jim and Harvey try to track down a bomber who leaves riddles to his crimes. Meanwhile, Oswald pays old friends a visit and is reunited with the father and family that he never knew.
While Jim adjusts to life in prison, Harvey makes plans to break his friend out. Meanwhile, Oswald adjusts to family life but discovers that his new relatives have other plans.
Jim discovers who framed him, but it may cost him his life. Meanwhile, Alfred gives Bruce an ultimatum, and Hugo releases Barbara from Arkham.
Bruce decrypts some of his father's computer files and learns of the mysterious Pinewood Project. While he and Alfred investigate, Barbara offers to help Jim find the mysterious Philosopher.
Hugo figures out the key to controlling the resurrected Theo and sends him forth as... Azrael. Meanwhile, Jim tries to convince Barnes that Hugo is responsible for creating monsters, and Bruce begins to learn that the law is insufficient to deal with the threats to Gotham.
Bruce convinces Selina to break into Arkham and rescue her friend Bridgit, and along the way Selina encounters an escaping Edward. Meanwhile, the manhunt for Azrael continues and Tabitha agrees to help Jim and Harvey track her brother down.
Bruce, Jim, and Lucius sneak into Arkham to try and find Selena, but Hugo realizes what they're up to and captures them. Meanwhile, Selena offers herself as a servant to Firefly, and Alfred turns to Harvey for help.
Hugo is ordered to destroy Arkham to cover the council's tracks, but Fish's efforts to escape complicate things. Meanwhile, Basil distracts Harvey from investigating Arkham, and Bruce and Lucius fail Edward's quiz.