Oswald controls Gotham by handing out licenses to criminals and lowering the crime rate. Meanwhile, Bruce continues his field training by preying on criminals, and Harvey tells Jim in no uncertain terms to let the licensed criminals go free. And a new gang tries to undermine Oswald by breaking Jonathan Crane out of Arkham and using his father's fear gas formula.
Bruce's efforts in fighting crime prove less than successful until Lucius steps in. Meanwhile, Jonathan Crane goes on a rampage through Arkham as the Scarecrow, and Jim goes in alone to stop him. Elsewhere, Tabitha and Selina receive an invitation to join a new criminal enterprise.
Jim acquires an unexpected ally when he travels to Miami to get Carmine to help him against Oswald. Meanwhile, Oswald ships an antique knife into the city and several interested parties seek to obtain it.
Bruce goes to a museum curator for information on the knife, but the man is soon killed and his grandson goes on the run. Meanwhile, Edward tries to come up with a riddle worthy of his nemesis, but things don't go as planned.
After six months in a coma, Butch is exposed to Indian Hills chemicals and transformed into a man-monster. Meanwhile, Bruce seeks out Ra's, and Sofia tries to make amends with Oswald.
A serial killer goes after crooked cops, putting pig masks on their corpses. Jim and Harvey hunt him down once they realize who his targets are. Meanwhile, Oswald suspects that Sofia is preparing to betray him, and Edward asks Lee for help.
The hunt continues for Pyg, who abducts three cops. Meanwhile, Bruce receives an invitation from a former classmate, and Selina sets out to prove she and Tabitha can still serve a role in Barbara's organization.
When Oswald learns that Edward is mocking him on stage at Cherry's, he tells the Sirens to bring Edward to him. However, Grundy protects Edward until Tabitha reminds him of who he was. Meanwhile, Jim receives an offer from the mayor and has to consider whether to go against Harvey or not... and what it will cost him.
Professor Pyg continues to torment Gotham city, involving Jim Gordon whenever possible. Sofia and Penguin get ready for a fundraiser for the orphanage, and things don't go as planned when Professor Pyg shows up as the chef. Meanwhile, Bruce's partying gets in the way of his relationship with Alfred.
After learning that Jim and Sofia are involved, Oswald prepares to torture Sofia for information about her plans. Meanwhile, Lee and Edward pay a visit to a gangster trying to move in on the Narrows.
Jim tries to stop the war between Oswald and Sofia, and discovers that the only way to do so is to take Sofia's side. Meanwhile, Tabitha attempts to beat Grundy's memories of Butch back into Grundy's head, and Alfred and Bruce come to blows.
A new killer, the Toy Maker, strikes at Lee's Narrows meeting. While Jim tries to determine the killer's next target and who hired him, Selina meets two old friends. Meanwhile, Alfred makes a new friend while wandering the Narrows.
Ivy learns of a secret project at WayneTech that will let her avenge the murdered plants of Gotham, and gives Bruce a dose of her hallucinogenic poison. While Bruce sees his real self, jim tries to track down Ivy. At Arkham, Jerome tries to convince Oswald to cheer up.
Ivy prepares to take revenge for the plants and for herself, and her first target is Harvey. While Selina prepares to confront her former friend, Bruce asks Alfred to help him while Edward comes up with a way to destroy Riddler once and for all.
Jim and Harvey try to track down Oswald, who has information on the man who can provide them with evidence to tie Sofia to Pyg. Meanwhile, Riddler and Oswald turn to Lee and Grundy for help, and Selina asks Bruce for help returning some stolen jewelry.
Jerome escapes from Arkham with Mad Hatter and Scarecrow, and goes after his uncle while Jarvis commands thousands to kill themselves at midnight. Meanwhile, Bruce searches for Jerome and the League of Shadows confront Barbara.
While Jim and Harvey chase after Jerome and try to find his target, Lee challenges Riddler to a duel of riddles. Meanwhile, Oswald tracks down Butch and offers him a cure to his monstrous condition.
Jerome plans his revenge against Gotham, and lies further plans in case of his death. Meanwhile, Barbara and Tabitha come to a parting of the ways, and Alfred helps Bruce celebrate his birthday.
The League uses Bruce's blood to bring Ra's back to life. Meanwhile, Oswald advises Riddler to turn against Lee, who is giving the money from the bank robberies to the people of the Narrows.
Jerome sends his followers a message from beyond the grave, and they hold a wake in the GCPD. Meanwhile, Jeremiah shows Bruce his new "clean" generator, and Butch grows impatient with Oswald's failure to find him a cure for his condition.
Jeremiah carries out his plan to destroy Gotham, while Lee and Riddler find Jim and tend to his injuries. Meanwhile, Oswald senses an opportunity and convinces Barbara and Tabitha to help him.
Ra's and Jeremiah join forces to destroy Gotham and recreate Bruce. Meanwhile, Jim faces off with the military when the mayor orders Gotham's evacuation, and Strange finds a cure for Butch.
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