Scarecrow was one of the Arkham inmates on the Joker's "party list" and was released during the Clown Prince of Crime's takeover of Arkham Island, both to distract Batman and for the Joker's general amusement, as Crane's experiments often left his victims dead of heart attacks. Crane made use of his secret stash of Fear Toxin, intending to break Batman this time. A fake patient session the Joker had with Batman suggested that Crane had been studying Batman with the Joker, but both were confused as to why Batman hadn't snapped and come over to their side yet.
Batman tracked a kidnapped Commissioner James Gordon to the island's Medical Facility. While Batman saved the staff, Joker refers to Crane as one of two "old friends" coming to the party: "one will be absolutely terrified if you leave without saying hello." After he rescued the staff, Batman took out a raiding party of henchmen before he took the elevator to the lower levels to follow Gordon's forensic trail of tobacco. The Joker taunted Batman through the Asylum's CCTV system, and considered releasing the elevator from its cables as a joke. As Batman made his way into the basement levels, he began coughing due to a colorless gas being pumped into the elevator; "prepare to face your greatest fears... All of them!"
Scarecrow had already gone to work with torturing new victims for research data, injecting them with his Fear Toxin and watching as they all died of heart-attacks before fleeing into another part of the building. Noting that the "good doctor" had started work early, Joker laughed that Batman would be buzzed through for his "appointment" when Scarecrow was ready, going on to ask what the Dark Knight feared most.
Batman used the vents to bypass the doors, finding Commissoner Gordon calling for help through one of the grates. Moments later, Batman emerged from the vents to find the corpse of his dear friend. His mind reeling from one of his greatest fears, Batman attempted to call Oracle to inform her, but was met with an automated message telling him that her number was not in service. Batman attempted to hunt Scarecrow down, only to find himself in the Morgue, where he was confronted by the reanimated corpses of his parents and a twisted obstacle course that was overseen by a giant, omnipotent Scarecrow. After he realized that he was experiencing a Fear Toxin-induced hallucination, Batman overcame the delusion by avoiding the Scarecrow's fiery gaze, and shined a Bat-Signal — a symbol of his willpower — directly into Scarecrow, temporarily defeating the hooded villain and freeing himself from the hallcuination.
Batman returned to his senses, just in time to discover that Scarecrow was long gone; the most likely explanation is that the Fear Toxin in Crane's syringes had run out, and he needed to refill them before making another attempt to break Batman. The Dark Knight returned to the corpse he thought was Gordon, but found it was actually a security guard; the Fear Toxin had affected Batman's mind more than he had thought.
Over the course of the night, Batman uncovered the mystery of the Titan Formula and investigated the Arkham Mansion to either find Dr. Penelope Young or to destroy her notes. Although he succeeded in the latter, the Joker wasn't outdone yet, and sent Victor Zsasz after Dr. Young. Batman raced off to find her, but was gassed by Scarecrow again, trapping Batman in a hallucination of the night his parents were murdered. Batman walked down a seemingly never-ending hall that turned into Crime Alley. Hearing the voices of his parents and their murderer, he fell to his knees and tuned into his nine-year-old self, kneeling before his parents corpses. He overcame this part of the delusion by remembering the kind words of a younger Gordon, returned to his adult state, used all his skills to once again avoid the Scarecrow's gaze, and temporarily defeated him with the Bat-Signal. Batman managed to free himself a second time, discovering that he had gotten himself trapped inside the belfry. This also made him too late to prevent Zsasz from taking Dr. Young hostage in Warden Quincy Sharp's Office.
As the night wore on, Batman learned from Poison Ivy of a plant spore in the Asylum's sewer system that would help him concoct an antidote to the Titan Formula and returned to the Intensive Treatment Center to retrieve it from Killer Croc's Lair. As Batman made his way to the elevators, he began coughing from the Fear Toxin again and experienced a strange kind of vertigo: his vision was filled with static to the distorted sound of the Joker's laughter. At this point, Batman began reliving the earlier events of the night, but in Joker's place.
The Joker arrived at Arkham in the Batmobile with a handcuffed Batman in the passenger's seat. The Joker took Batman to the Intensive Treatment Center. Batman ranted and raved, insisted that he hadn't killed "that family," and demanded to be cut free. He resisted Crane's attempts to examine him, leading Scarecrow to declare him a lost cause. Left to the Joker's mercy, the Clown Prince of Crime aimed his gun at Batman's head and fired at point-blank range.
After he realized that he was suffering yet another Fear Toxin hallucination, Batman climbed out of his own grave and made his way past the cells that were full of other insane Batmen to find the Bat-Signal. Just like last time, Crane made Batman see him as an omnipotent giant that could kill him with a single palm strike; he even called in henchmen to attack him, but Batman beat them easily. About to break Batman's mind, Crane was shocked when Batman shined the Bat-Signal.
Free of the illusion, Batman grabbed Crane by his hood. However, Scarecrow plunged his syringes into Batman's gauntlet, dosing the Dark Knight with more Fear Toxin to fight off. The illusion now had the giant Scarecrow watching Batman resist numerous skeletal attackers, including two Titan-enhanced henchmen. With Batman occupied, Scarecrow fled into the adjacent corridor; the bars would keep Batman at bay the next time he broke free.
Every time Batman defeated a number of enemies, one of the three Bat-Signals would activate and damage Scarecrow. Batman prevailed yet again, and defeated as many skeletal warriors as needed to strike Scarecrow with the three Bat-Signals. Scarecrow was left shocked by this turn of events as Batman once again gripped his hood through the bars. He gave Batman another quick injection of toxin, buying himself time to flee to the elevator with a pouch full of his toxin.
As Batman regained his senses, Crane taunted him, asking why the Dark Knight couldn't see that the relationship between him and the super criminals was symbiotic - they need each other. Crane rode the elevator all the way down to the lowest level to access the sewers, unaware that the sewer system served as the lair of Killer Croc. Joker's henchmen locked the door behind him, hoping Croc would eat Crane, as they find him creepy; however, Batman pummeled them and unlocked the door.
As Batman examined a Titan-mutated plant, Scarecrow appeared and warned him to stay away, threatening to drop the bag of Fear Toxin into the underground river, which would fill the cave with Batman's worst nightmares and, even worse, contaminate Gotham's water supply for 100 years. Before Scarecrow could make good on his threat, Killer Croc burst from the water and grabbed Crane, having mistaken him for a guard, a stray inmate, or Batman. Scarecrow lost his grip on the Fear Toxin and dropped it harmlessly to the ground.
Fearing for his own life, Scarecrow flailed hopelessly to get free of Killer Croc's grip. Right as the monster was about to take a bite out of him, Batman saved Crane by throwing a Batarang at Croc's electrified collar to briefly activate it. Though the zap from the shock collar stopped Croc from eating Scarecrow, he still refused to let go, and dove back into the water with a screaming Crane in his grip.
To Scarecrow's bad luck, the collar's zapping angered Croc. In retaliation, Croc severely mauled Crane's face. Batman again saved Crane's life from Croc when the mutated man-eater detected the Dark Knight's footsteps on the floating planks deeper in the sewers. Croc left Crane to die of his injuries in favor of killing his main target: Batman.
In Arkham Asylum, Scarecrow closely followed his over-the-top comic book portrayal: a downright, sadistic villain who took glee in murdering innocent people and/or driving them into insanity, complete with a high-pitched voice with a loud and dramatic tone to it. As evidenced by his Interview Tapes, Scarecrow was extremely intelligent and manipulative, as he managed to convince at least two of his doctors that he wasn't actually insane. This included Dr. Young, who even entertained the possibility that he was innocent. Scarecrow displayed a respect for the concept of fear that bordered on veneration. He believed fear to be the driving force in people's lives, saying that almost every action you took was a byproduct of fear, and wanted to prove his megalomania by using fear to control others. This is further shown in Arkham Knight where after detonating the Cloudburst, drowning Gotham in his toxin he proudly describes it the "city of fear" and "my domain."
Unlike many of Batman's foes, who commit crimes in order to gain money or power, Scarecrow's only motivation seemed to be a compulsive need to cause fear in others. In his interview tapes, Dr. Kellerman stated that the only thing Scarecrow seemed to care about was his "research." This is exemplified by Scarecrow treating their therapy sessions as though HE was the doctor, and Kellerman was his patient. Scarecrow would even create interview tapes of his own while observing his victims, and expressed fascination in understanding the root of their fears while showing no concern for their safety or wellbeing. Even in the middle of being captured by Batman, Scarecrow desperately asked him what he saw while under the effects of his toxin in order to continue to "study" its effects.
Jonathan Crane, in his Scarecrow outfit, wears a long, brown burlap-like coat that is torn and frayed in several places. Underneath, he wears dark pants similarly distressed and showing signs of wear and tear, suggesting a rough and lived-in appearance. A simple rope belt cinches his waist, from which a small, roughly sewn burlap sack hangs. The rope is thick and braided, slightly frayed at the ends, contributing to the overall sense of roughness and age. His footwear is also wrapped in similar beige bandages, secured around his ankles and finishing at the tips of his shoes, which look worn down. He has a elaborate contraption attached to his gloved hands. It is a complex mechanical device with multiple syringes filled with a glowing orange-red liquid connected by translucent green tubes. These syringes protrude from the fingers, giving the hand a menacing, claw-like quality. The device emanates a faint, orange glow.