He was briefly seen when Shredder and Ra's al Ghul passed through the facility. He was later freed by the Joker, who sprayed the dangerous inmates with mutagen. Crane was transformed into a mutant crow, and subsequently went to the boiler room to wait for his enemies.
He was found by Leonardo and Batman, and managed to dose the Turtle with his signature fear gas, causing him to hallucinate that Crane was murdering his brothers and taunting him. While Leonardo was unbalanced, Crane took the opportunity to further torment him by knocking him down. Fortunately, Batman was able to reach through Leonardo's hallucinations, and Leonardo was able to knock Crane out with his sword.
Though not shown, he was presumably demutated by the police once it was confirmed that the retromutagen was non-lethal.
- Scarecrow's voice actor, Jim Meskimen, also voices Commissioner James Gordon in the same film.