Scarecrow was one of the earliest enemies of the Batman.
Jonathan Crane was often experimented on by his father, a doctor who researched fear. Becoming obsessed with the topic himself, Crane attended university, but an illness of insanty took over and by the time Crane became a professor, the Batman had arrived in Gotham City. Fully insane, the mad professor became the supervillain known as Scarecrow and began to make poisons while teaching at Gotham State University. Allying himself with the Penguin, the two tortured Linda Friitawa into becoming Fright. With the notoriety of his Scarecrow identity growing, Crane attempted to conceal himself by working with the GCPD. After abducting his entire graduate class, though, Scarecrow was exposed as Crane by Batman. When encountered by Batman and Robin the first time, Crane managed to escape by dousing them with his Fear Toxin. Escaping to the farmlands outside of Gotham, Scarecrow once again eluded capture by spraying Robin with the fear gas. Heading off to a church in the city, Crane met up with the Orphan and Cassandra Cain, who prepared him to go to Prague. Scarecrow fled the United States but was pursued by Batman. For his crimes, Scarecrow was arrested by the GCPD after being defeated by the Batman. Incarcerated in Arkham Asylum, like almost all others, Crane escaped.
Scarecrow would ally with the supervillain mastermind Bane and develop a new Fear Toxin that would be mixed with Bane's venom. The toxin would be used in a plot against Batman that would culminate at Harmon Island, the Scarecrow would escape only to learn of Bane's failure. Scarecrow would then discover that Eli Strange, the son of Hugo Strange, would have taken the Anti-Fear Toxin Pills developed by Batman as well as the ingredients for his new Fear Toxin. Scarecrow, in a twisted effort to save Eli from being corrupted by the Gotham City Underworld, enlisted the help of Batman. Scarecrow would send Batman on a cat and mouse chase, but would eventually be caught and would reveal the truth. Screacrow was tied up by Batman, despite having nothing charged against him and his presence in the Harmon Island incident having gone unnoticed, and sent to Arkham.
Crane was freed from Arkham by Graves who would proceed to extract information about Batman from him. Staying free, on Halloween, Scarecrow's usual time to evoke fear, the Batman managed to trick Scarecrow into going to the abandoned Arkham Detention Facility for Youth. There the Scarecrow met up with the Mad Hatter and the Penguin. Though they were not captured by the Batman, they were convinced the Dark Knight was hunting them and were fearful the entire night.
Very soon after, Scarecrow, freed, began to terrorize little children near half to death, and took the guise of Hollow Man. However, Scarecrow ditched this guise very quickly and ended up kidnapping Commissioner Gordon. Scarecrow's plan to set loose the Fear Toxin on all of Gotham was stopped at the last minute by Batman. On his way to Arkham, Crane was freed by the Outsider who asked for Scarecrow to join the Secret Society in order to enact fear for him. After his acceptance, Crane was returned to Gotham, and took control Arkham Asylum with his new Contentment Sedative. Using this sedative, Scarecrow plunged Gotham into the world of Gothtopia and was nearly able to once again unleash Fear Toxin on Gotham. Due to Poison Ivy allying with Batman, however, Scarecrow's plans were put to an end. After the events of the Trinity War had left the world to the villains, Crane's first task as a Secret Society member was to go and offer to Two-Face an invitation to the Secret Society, with his last to invite John Corben as well. Crane then divided Gotham City up amongst all of the other inmates from Arkham Asylum, declaring the city to be his. He also prepared for a civil war within the Society with the only being powerful enough to challenge him, his former partner Bane. However, even when Bane arrived, Scarecrow had not fully accomplished all of his preperations. During the Arkham War, Crane nearly accomplished victory, but was defeated by Bane who ended up stringing him across the streets of Gotham. When all the madness of the Society was said and done, Scarecrow returned to the streets to test out the Fear Toxin on random people. One of these people was an amnesic Batman who had no memory and so no fear and tried to shoot Scarecrow with a gun. Later causing an explosion that resulted in some deaths, Scarecrow was shortly thereafter once again apprehended.
Taken back to Arkham Asylum, Crane began to notice that everything was going wrong. Realizing that Arkham had changed due to the presence of the Joker's Daughter, Crane began to fear for himself. He was then captured by the Daughter, who prepared his execution. Crane was not executed, however, and was one of the many criminals who attempted to escape Arkham when it fell. Once again managing an escape, Scarecrow began to work on a new dose of Fear Toxin, dubbing it the Cassandra Strain. In his next meeting with Batman, the strain failed to have any immediate effects and Crane was once again captured.
Crane was obsessed with understanding the concept of fear. He wanted to discover what made fear so important and how to manipulate the chemicals that spurned in one's brain when they felt fear. As a means to his ends, Crane developed his Fear Toxin to study this further.