Maybe Joker was one of Crane's patients in the ward that busted out when Batman went through there in BB.
Joker could've been one of Crane's patients on which the fear gas had little effect, so he kept upping the dose/strength of it, trying to break him...but it just made him more of a nutjob. Like the first time Crane uses the gas on him (in flashback) and puts on the Scarecrow mask...there's a pause as the patient clears his sinuses, and he just starts laughing hysterically at the mask and making fun of him. Could be a funny moment, but a cryptic one as well.
They end up working together, but Joker remembers everything and at some point turns the tables, torturing Crane in a mock psyche session, using the fear gas as part of it. Could be a good oppportunity to do some really wild visual/hallucination stuff with the Joker face. Might even be a good way of introducing the Joker as 'the Joker', once his face becomes the way it is...with him taking off Crane's Scarecrow mask to reveal his own gharish face...then it turns into a horrific hallucination as the gas takes effect. Maybe.