After he is pushed out of the GCPD Jim Gordon turns to Penguin -- flush with new-found power -- for help getting back in. While Bruce Wayne struggles to gain access to a secret room inside Wayne Manor, Barbara adjusts to her new life inside Arkham Asylum.
While Galavan torments the Mayor of Gotham, the criminally insane Jerome leads a team of escapees from Arkham in a plan to strike terror in the heart of the city. Bruce and Alfred clash over how to move forward, and Gordon asks Harvey Bullock to come back to the GCPD.
While Gordon and Bullock try to track down Jerome in the wake of a devastating attack, Alfred and Bruce attend a magic show at the Gotham Children's Hospital gala -- which turns into a hostage situation when Galavan initiates the next phase of his plan.
A new police Captain arrives at the Gotham PD to clean house and form a new special task force, while Galavan attempts to bring Penguin in on his plan for Gotham's future. Galavan introduces Bruce Wayne to a new friend, and Nygma asks Ms. Kringle to dinner.
Penguin is pushed to recruit a dangerous family to conduct a series of arsons, leading him to a revelation about Galavan and his true agenda in Gotham. Barnes' task force continues to put the squeeze on Penguin's operation.
Selina tries to help her friend Bridgit get out of town, only to see her brothers reassert their control over the Firefly. Meanwhile Butch tries to infiltrate Galavan's organization, and Nygma and Miss Kringle take their relationship to the next level -- leading to unexpected consequences.
After Oswald finds his captive mother he learns where Butch's loyalties lie, as Galavan moves to use the police force against Penguin. Nygma discovers that his alter-ego has more pull than he thought after a body goes missing.
Barbara turns herself in to the GCPD as part of a plot to lure Jim Gordon into a trap, while Galavan makes an emotional appeal to buy Bruce's share in Wayne Enterprises. Nygma takes a trip into the woods.
Gordon finds himself in the crosshairs of the city's most dangerous hitmen after Tabitha Galavan puts out a hit him. Nygma tries to bond with Penguin as he nurses him back to health, and Alfred tries to prevent Bruce from seeking out Silver St. Cloud.
With Galavan in jail Detectives Gordon and Bullock pursue a criminal cult that has arrived in Gotham to "cleanse" the city. Bruce goes to great lengths to convince Silver to find out the name Galavan was going to give him.
As the Order of St. Dumas is poised to kill Bruce Wayne in a ritual sacrifice, Penguin appeals to Jim for an alliance against their common enemy. Meanwhile Alfred fights to stay alive, and Silver is given one final task to prove herself to the family.
Gordon returns to duty after the death of the new Mayor under suspicious circumstances, but Penguin's emergence from hiding complicates things. While Oswald settles in at Arkham Asylum, a desperate cryogenicist named Victor Fries uses advanced freezing technology to experiment on innocent people.
The GCPD takes Victor Fries' wife Nora to Arkham in a ploy to lure him in, but cannot prepare themselves for the fury of his onslaught. With new intel on the man he believes killed his parents Bruce must decide what sort of man he is going to become, and Penguin struggles under Hugo Strange's "treatment."
With help from Alfred and Selina, Bruce confronts the man he believes killed his parents. While Detective Gordon initiates an investigation into the disappearance of Kristen Kringle, Hugo Strange continues his treatments on Penguin.
Gordon and Bullock investigate a museum heist that points to a train station bombing, unaware that the newest threat to the people of Gotham is someone close to them. An apparently reformed Penguin visits his old acquaintances, and Selina and Bruce attempt to steal some cash. Meanwhile, Jim learns that the investigation into Galavan's murder has been re-opened.
Jim faces a difficult prison sentence, with the city's criminals and even the warden gunning for him. Elsewhere, Oswald struggles with his personal demons as he gets to know his father better -- while his new family plots against him.
Gordon's quest to clear his name puts him on the trail of the real killer, prompting him to turn to Edward Nygma for help. Oswald makes a discovery about his father's true fate, leading to a confrontation with his new "family."
Jim finds himself reluctantly paired with a rehabilitated Barbara while looking for new information on the Wayne case. Meanwhile, Bruce follows his father's files to a woman who has been subjected to disturbing experiments.
After Jim Gordon confronts Hugo Strange about his past connection to Thomas Wayne, Strange finds a way to manipulate the newly-resurrected Galavan to his own ends -- forging him into a super-powered assassin.
Jim and Harvey confront Dr. Strange about Azrael, who is on the loose in the city with a rekindled mission to kill Bruce Wayne. While Alfred tries to protect his charge from the assassin, Selina Kyle infiltrates Arkham to try and rescue a friend.
With help from Lucius Fox Bruce pays a visit to Arkham Asylum for a very personal meeting with Hugo Strange, who is under pressure from his mysterious employers to find a viable way of bringing back the dead -- including one Fish Mooney. Elsewhere Selina tries to find a way to save her friend Bridgit, a.k.a. "Firefly."
Having been replaced by a doppelganger Gordon finds himself trapped inside Indian Hill, along with Bruce and Lucius Fox, as Strange and his superiors plan for the facility's total destruction. Fish uses her newfound power to make a play for freedom.
