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There is nothing to fear... but fear itself!
Boo! Aw, having trouble? Take a seat. Have a drink. You look like a man who takes himself too seriously. Do you want my opinion? You need to lighten up.
~ Scarecrow to Batman after exposing him to the fear toxin.
Dr. Jonathan Crane, also better known as Scarecrow, is a major antagonist in The Dark Knight Trilogy by Christopher Nolan, serving as the secondary antagonist of Batman Begins and as a minor antagonist in both The Dark Knight and The Dark Knight Rises.
Dr. Jonathan Crane was the chief administrator at Arkham Asylum, and was secretly working with both Ra's al Ghul and mob boss Carmine Falcone, who brought shipments of drugs in for Crane to use to create his Fear Toxin. He would work again with the League of Shadows years later when Bane and Talia al Ghul go to Gotham City with the intentions to destroy it.
~ Crane, revealing his true identity to Carmine Falcone.
Dr. Jonathan Crane started off as a university professor in psychology. He took advantage of his profession by testing his "Fear Gas" on his students, driving them into insanity. He was finally exposed and fired after one of his students jumped through a window to assault a Santa Clause mannequin. Wanting to protect their reputation, the university fired him in secret. It was then that Crane started working at Arkham Asylum where he'd subject the patients to the same treatments.
In order to maintain Carmine Falcone's participation, Crane had Falcone's thugs, including Victor Zsasz, declared insane and moved into Arkham Asylum, rather than facing criminal charges, which Assistant District Attorney Rachel Dawes found highly suspicious.
Later in the film, after Falcone was captured by Batman and imprisoned in the Blackgate Penitentiary, he slit his wrists in order to get an insanity plea. When Crane was summoned to inspect him, Falcone attempted to blackmail him into letting him in on his and Ra's al Ghul's plan. Instead, Crane put on his Scarecrow Mask and gassed Falcone with his Fear Toxin, which left him in a state of psychosis and had him moved to Arkham Asylum on suicide watch.
When Rachel heard about Falcone being moved to Arkham, she was once again suspicious. She personally went down to Arkham to meet with Crane and believed Crane himself to be the one responsible for Falcone's condition. Rachel informed Crane that she had arranged for a doctor from County General to have their own evaluation of Falcone that same night and to be on the Judge's desk by the next day. Crane took Rachel down to the basement level and showed her where his Fear Toxin was created. Frightened, Rachel attempted to escape, but Scarecrow caught up with her and gassed her with a consecrated dose of his Fear Toxin. However, before he could continue experimenting on her, Batman arrived, battled Scarecrow, and eventually gassed him with his own Fear Toxin and learned that he was working for Ra's al Ghul. Crane was eventually put in a straitjacket and imprisoned within Arkham itself.
Near the end of the film, when the League of Shadows released the Arkham Asylum inmates, Scarecrow was freed as well, and when the Fear Toxin was mass-released into the air by Ra's, he was encountered riding on a horse he stole from an officer he killed by Rachel and a young boy as a demonic-looking rider. As Scarecrow tried to attack them he was shot in the face by Rachel using a taser, paralyzing him and provoking his horse to run away with him on it.
After Ra's plan is foiled, Scarecrow is confirmed still at large with Batman tracking him.
Selling his Fear Toxin
Buyer beware. I said my compound would take you places. I never said they would be places you wanted to go.
~ Scarecrow in The Dark Knight.
Scarecrow briefly appeared at the beginning of The Dark Knight and was still on the run after being released in the previous movie. Before Batman focused on battling against the chaotic anarchist, The Joker, he learned that Scarecrow attempted to sell his Fear Toxin to The Chechen, a crime boss who operated in Gotham and was also an ally of the Joker's but was interrupted by a group of Batman impersonators. In the novelization, he tested his Fear Gas on a junkie and murdered him before selling them as hallucinogens. Scarecrow could immediately tell that those weren't the real Batman because they had guns (something which the real Batman didn't use). Eventually, Scarecrow spotted the real Batman. In the chaos, Scarecrow attempted to escape in a van. However, the real Batman caught up to him and successfully captured him, by dropping on top of the van. Scarecrow and the other criminals were left for the police and were finally imprisoned.
Death or exile?
In The Dark Knight Rises, set 8 years after the previous movie, Crane appeared as a minor antagonist, following Bane's launching of Gotham City into anarchy. After being set free from Blackgate Penitentiary, Dr. Crane served as a judge for mock trials against the rich and powerful of Gotham City's citizens, who usually offered the options death or exile, which both lead to the victim's deaths.
He was first seen judging Philip Striver who chose exile but died regardless and later appeared to judge Gordon and his cops who chose death, but Crane sentenced them to exile anyway knowing it would result in their deaths regardless. However, Batman returned to Gotham in time to save them and rally them against Bane and save Gotham. After the conflict Scarecrow's fate is unknown but he was either sent back to Arkham Asylum or is now at large once again.
Jeff Goldblum, Ewan McGregor, Marilyn Manson, Nicolas Cage, Jeremy Davies, and Christopher Eccleston were all considered for the role of Scarecrow before Murphy was cast.
In the novelization of Batman Begins, Scarecrow is even more evil than his movie counterpart as he's well aware of the League of Shadows' plan to drive Gotham into wiping itself out in fear-induced insanity and looks forward to using the millions of civilians as a "test" for his gas-unlike in the film where he thinks they're just going to blackmail the city for ransom.
It was because of this incarnation of the Scarecrow that the Scarecrow wasn't allowed to appear in the Cartoon Network television show The Batman, as the Bat-embargo didn't wish to confuse the viewers even though the design was going to not look similar at all with this Scarecrow.
Scarecrow was one of two main villains in The Dark Knight Trilogy who didn't die, the other being the Joker.
Scarecrow was the only villain that appeared in all three of Christopher Nolan's The Dark Knight Trilogy. Some viewers believe that maybe he was featured in the three films as one of the trilogy's core themes is fear.
He appears also in one of the short films in the short film collection Batman: Gotham Knight, which is supposed to be canon with Christopher Nolan's films. However, given the many tonal and content-based inconsistencies with Nolan's films that are in Gotham Knight, just how canon or compatible with Nolan's films Gotham Knight is remained ambiguous.
Cillian Murphy auditioned to play Batman but Christopher Nolan instead gave him the role of Scarecrow.
Although the Scarecrow's fate was left ambiguous at the end of The Dark Knight Rises, Cillian Murphy believes that Scarecrow survived the film's events and is still out there. However, as The Dark Knight Trilogy ended with that film and is disconnected from the recent Batman films, it's highly unlikely that we will see the Nolanverse's Scarecrow ever again.