Scarecrow's fear toxin was forcing Joker's personality to take over intentionally.

“I don’t know why you’re resisting death. After all, you and I both know you haven’t got much longer to go anyway. Before he died the Joker informed me that he infected your blood. I designed a very special form of my fear toxin to bring out the Joker in you.”

“He’s right, Bats. We were working together. So, tick tock, your time is running out. Madness and fear is what your future’s all about.”