There, he reveals to Penguin that the other Legion members anticipated his betrayal and that he knew Penguin would go to Jim Gordon, and then proceeding to knock him out. Later, Scarecrow, Mad Hatter and the Penguin go to a hangar to load the laughing gas onto a blimp and release it upon Gotham.
Freeze, carries out a raid on Wayne Enterprises' chemical lab to brew more of the dangerous toxin. In "That's Entertainment," Scarecrow, along with Mr. At the end of the episode, it is revealed that Jerome secretly tasked Scarecrow to concocts a laughing gas for him to spread across the city. He and the Mad Hatter break out Jerome from his twin brother Jeremiah's custody but are chased off by Gordon and Bullock. In " Mandatory Brunch Meeting," the Scarecrow is one of the criminals assembled by Jerome to be part of his "Legion of Horribles".
After the Hatter is defeated by Jim Gordon, Scarecrow gasses the driver of his transport as he and Jerome free him for their next plot. He is freed by the Mad Hatter where they, along with Jerome Valeska, collaborate in a plot that involves releasing all the inmates of Arkham Asylum. In " One of My Three Soups," Scarecrow is shown as an inmate at Arkham Asylum after getting apprehended at some point. After Gordon turns on the sprinklers and neutralizes the fear gas' effects on the inmates, Scarecrow got away. When Gordon confronts Scarecrow, he gets infected with fear gas until he overcomes it. In " The Fear Reaper," Crane invades Arkham Asylum and uses the fear gas on Warden Reed and other inmates causing the guards to flee. He then wreaks havoc on Gotham with the toxin as "The Scarecrow". Jonathan eventually embraces his fear and uses the toxin against Grady Harris after Merton and his fellow gang members were arrested. A gang of criminals led by Grady Harris and Merton bribe Reed to give them Crane and forces him to re-create his father's fear toxin so they can use it to control Gotham City. He is next seen in the season four episode " Pax Penguina," in which he is institutionalized in Arkham Asylum, where the corrupt warden Reed uses his fears to keep him under control. Detectives Jim Gordon and Harvey Bullock save Jonathan's life, but are too late to save his father and his sanity the toxin has left him in a state of perpetual terror, plagued by hallucinations of his greatest fear: scarecrows. His father Gerald Crane (portrayed by Julian Sands) creates the 'fear toxin', a serum designed to eliminate fear, and then injects Jonathan with it.
He is introduced in the first-season episodes " The Fearsome Dr. Thompson (in the second half of the fourth season as well as the fifth season).