As a young boy, Jonathan Crane had an interest in fear. Years later, he became a professor at Gotham University who then experimenting fear on students. Terminated by Gotham University for his immorality, Crane hatched a plan to reduce the University to shambles by causing the professors and board to constantly experience their greatest fears. Dubbing himself The Scarecrow (and adopting a costume along a similar vein), he chemically bombarded the university members who opposed him, reducing them to a paranoid state. His plans, however, came to ruin upon the intervention of Batman. Though he was able to incite the same fear within the hero, the Dark Knight overcame and imprisoned his foe.
Some time later, the Scarecrow escaped from Arkham Asylum. His funds all but dissolved, the scientist needed a quick source of cash. He created a chemical residue which turned adrenaline into fear; applying it to telegrams he personally delivered to star athletes, he gambled against those athletes (or their respective teams) and began raking in quick cash. The fear seemingly inexplicable, his plan progressed perfectly.
Unbeknownst to the Scarecrow, however, Dick Grayson shared a room with Brian Rogers at the University. Though Rogers underwent the same debilitating fear attack after receiving the Scarecrow's telegram, at a crime bust, Robin underwent a similar attack. To Batman, the events seemed more than coincidental, and the Dynamic Duo investigated the scene. Discovering the ploy, the two once again apprehended the Scarecrow and imprisoned him in Arkham.
While in Arkham Asylum, the Scarecrow discovered Arkham's water supply in an underground cavern. Using this, he managed to continue his criminal operations while still assuming the guise of a psychiatric patient. Unlike his previous schemes, this time, he prepared for Batman's intervention. The first plan was to contaminate the Gotham Health Spa's water, information the Scarecrow had leaked to the Gotham underbelly. A henchman (in radio communication with the Scarecrow) performed the deed, and as Batman tried to stop him, both were sprayed with a mind-manipulation gas. Batman began hallucinating, and after an accident, was checked into Arkham Asylum.
With Batman out of the picture, the Scarecrow began the next phase of his plan: contaminate Arkham's water supply. From there, he would be able to study the effects of fear on a massive control group. Batman, however, escaped. Despite suffering constant hallucinations, he managed to halt the Scarecrow's operations and arrest the criminal once more.
The Scarecrow, like most of Batman's rogues, was present for the Trial of Batman as a member of the jury and a security guard. Likewise, he was also one of the numerous villains who suffered under Lock-Up's brief security regime at Arkham; indeed, he actually broke out just to get away from him. Later, when Lock-Up was apprehended, a pleased Scarecrow vowed to teach him new lessons in fear.
Much later, he developed a gas that did not cause fear; instead, it removed the essence of fear from the victim. After testing the gas on a few civilians and a disguised Bruce Wayne, the Scarecrow planned to hold Gotham ransom or the city would become chaotic with the absence of fear. Though Batman began ignoring his principles, Robin managed to subdue him and retrieve the antidote, and the two captured the Scarecrow.
Shortly thereafter, the Scarecrow attempted another heist. Though he was once again caught, he managed to spray Batgirl with one of his gases; the heroine entered a deep sleep and began living her greatest fear: a war between Batman and Commissioner Gordon over her participation and her death in the Dark Knight's mission.
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