(Arkham Asylum: Living Hell #1, 2, 6) - Crooked businessman Walter "Great White Shark" played the system, and was found not guilty by reason of insanity after a trial for defauding people out of their life's savings. Shark found that he was a little fish in Arkham, and the inmates, including Scarecrow, delighted in tormenting him. In the cafeteria Scarecrow stabbed White with a fork as an "experiment" in fear. The rest of the inmates were sick of White's whining, and a riot erupted. Doodlebug unleashed the Skarva, demons trapped under Arkham, and built a flame pit to open a gate to Hell. Aaron Cash tried to fight the Skarva, who turned Scarecrow and other inmates into monstrous versions of themselves to fight him. The demons returned to hell with the help of Demon Etrigan and Great White, and Scarecrow and the others were restored to normal. With disaster averted Jeremiah Arkham decided to blame the supernatural encounter on hallucinations brought on by Scarecrow's fear gas in order to save his staff's sanity. The incredulous Scarecrow was tossed into solitary confinement.

(Catwoman II #58-60) - Scarecrow was creating a new fear toxin that binded to estrogen from his Arkham cell. He had a letter sent to him coated in toxin, causing the guard who delivered it to develop a fear of glass, making him shoot out the front of Scarecrow's cell and allowing him to escape. Scarecrow hated that Gotham seemed used to fear after the cataclysm, so he wanted his new fear toxin to be extra potent, but the woman he tried it on died. He knew he needed a tougher test subject, and chose Catwoman, holding her fence hostage. Catwoman started hallucinating about Headhunter, a man she'd been interested in who turned out to be a serial killer. She fled went home to sleep it off, but the visions kept coming, and she hated the feeling of helplessness they caused her. Scarecrow set up shop in a chemistry lan in Gotham State University, and had his goons bring him more test subjects, but they all died from femfear. He told his underlings to dump the bodies and bring him Catwoman, his curiosity was piqued at how she'd survived. Catwoman took out his goons and confronted Scarecrow, who was counting on his helpers to restrain ehr while he injected her. She'd been feeling fearless again, she told him she grew up being afraid, until she manipulated her fear and turned it into anger. She snatched away his syringe full of femfear, and injected herself. Catwoman hallucinated being locked up in Arkham, with the inmates telling her she was finally where she belonged. In the vision they brutally attacked her, until Batman came to her rescue, telling her she depended on him completely. This snapped Catwoman into reality, her greatest fear was dependency, something that couldn't just sneak up on her life most fears, and she burned Scarecrows notes containing years of research before tossing him out a window.

(Batman I #564) - Mikey's shooting didn't break Father Chris' congregation, so Scarecrow decided to take action. He tried to convince the churchgoers that they were in Hell and that God had forsaken them. After learning that Father Chris kept an arsenal in the church he leaked this information to the False Facers gang. When the gang prepared to storm the church Scarecrow urged the congregation to use the arsenal to fight back. His only goal was bloodshed and fear, seeing himself as doing the devil's work in a forsaken Gotham.

(Batman: Joker’s Apprentice #1) - Joker chose fellow inmate Arthur Rankle, a serial killer who raped and killed eighteen women before Batman took him down, as his apprentice. After teaching him everything he knew he was ready to unleash his pupil on Gotham. Joker said Arthur would be free soon, and warned him never to confront Batman in the dark because it was his natural habitat. Joker alerted Scarecrow’s crew when their boss was scheduled for pickup for court and they agreed to bust out Rankel along with Scarecrow. Joker gave Arthur his diploma and bid him good luck. On the outside Arthur read his diploma, finding ways he could contact the Joker via a pay phone or e-mail, and keys to one of Joker’s hideouts, the former film studio of Slaphappy films. Arthur settled in, planning his big debut and his next kill. He started talking to a rat he named Lassie. He told the rat all his thoughts, how he was in control and the Joker was not, and how he chose to kill unlike Batman’s rogues gallery, and could stop himself at any time. He told Joker he’d need two men to help him carry out his big kill, and Joker sent him Dr. Thomas DeGeorge, a doctor who was locked up after it was discovered he was causing seizures in his patients so he could save them and seem a hero, and Calvin Marshall. They went on a killing spree but were brought to justice by Batman.

(Spectre IV #11) - Arkham; Scarecrow hallucinated and cowered in fear while one of Spectre's (Hal Jordan) aspects struggled to find a way to redeem Scarecrow’s soul.

(Batman: Gotham Knights #38, 39) - Scarecrow was released from Arkham by David Said of Checkmate. He had Scarecrow and Mad Hatter I observe the imprisoned Huntress, and do a psychological profile of her so that Checkmate would have an edge when they offered her a government position. Said was so impressed by Scarecrow and Mad Hatter that he kept them out of incarceration and sent them to the nation of Hasaragua, where he hoped they could be used to topple that country's dictator.

(JLA #84) - The Burning, who needed fear and chaos to reproduce, unleashed a wave of fear and remorse that washed over the inmates of Arkham Asylum, including Scarecrow.

(Batman #617) -