Dr. Jonathan Crane, alias Scarecrow, is a psychiatrist and biochemical expert specializing in fear manipulation. He engineered a potent hallucinogenic fear toxin, inducing severe hallucinations based on victims' deepest phobias. This toxin became his signature weapon, exploiting psychological vulnerabilities over physical force.

Following the Narrows riot, Scarecrow remained active within Gotham City's criminal underground. He formed an alliance with the mutated Killer Croc, dosing him with fear toxin to exert control and amplify Croc's violent tendencies. Scarecrow targeted Cardinal O'Fallon, abducting him during a cathedral sermon. He subjected the Cardinal to a mock trial, condemning him for humanitarian work with Gotham's homeless, demonstrating Scarecrow's warped sense of justice and desire to punish perceived hypocrisy.

During a subsequent confrontation in the cathedral crypts, Scarecrow attempted to execute Cardinal O'Fallon. Batman intervened, leading to a physical altercation. Scarecrow escaped amidst the ensuing chaos, which included an explosion and flooding triggered by Batman. His methods frequently involved leveraging allies like the manipulated Killer Croc to achieve goals while avoiding direct combat.

Scarecrow's background includes prior contamination of Gotham's water supply with fear toxin as part of a scheme linked to the League of Shadows. Initially captured by Gotham City Police Sergeant James Gordon and Detective Arnold Flass, he later escaped during a mass breakout at Arkham Asylum. His obsession with fear, rooted in childhood trauma and abuse, drives his lifelong pursuit of mastering its psychological mechanisms. His criminal actions serve as continuous experiments to refine his understanding and control of fear.