Fish Mooney reveals a secret of Oswald Cobblepot's, prompting Maroni to take him on a trip to test his loyalty. Meanwhile, Gordon and Bullock hunt down a killer who targets victims with severe phobias and Bruce Wayne confronts Gordon for failing to make progress on his parents' murder case.

Gordon and Bullock set out to stop Gerald Crane, a biology teacher who has been harvesting the glands of his murder victims. Meanwhile, after finding herself in an unusual setting, Mooney continues plotting to gain power, and Falcone attempts to change Maroni's plan for the Penguin.

Gordon fears Jonathan Crane is still alive and back in Gotham, when The Scarecrow's signature MO is used in a series of robberies. Meanwhile, Penguin's "licensing" of crime in the city backfires during the grand opening of his new Iceberg Lounge. Also, in the aftermath of his encounter with Ra's Al Ghul, Bruce begins his vigilante watch.

Under pressure to prove that the GCPD is still powerful, Gordon attempts to bring in Jonathan Crane. However, Gordon puts himself in a dangerous situation at Arkham when he is forced to fight off lunatics and the demon within himself. Meanwhile, with Barbara's unexpected return, Selina and Tabitha must consider risks that come with joining her in the weapon business.