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By the end of The Dark Knight (2008), the Joker's fate is left open. Yes, he was arrested, but he is still alive. His fate is never completely explained. More precisely, in The Dark Knight Rises (2012) :
I noticed that Jonathan Crane/Scarecrow was the judge of Bane's tribunal. So, was the Joker also among the prisoners released by Bane from Blackgate Penitentiary or maybe Arkham Asylum?
Is there any material that explain what happened to the Joker between those two films?
In the novelization of The Dark Knight Rises the Joker is said to be the sole occupant of Arkham Asylum.
“Now that the Dent Act had made it all but impossible for the city’s criminals to cop an insanity plea, it (Blackgate Prison) had replaced Arkham Asylum as a preferred location for imprisoning both convicted and suspected felons. The worst of the worst were sent here, except for the Joker, who, rumor had it, was locked away as Arkham’s sole remaining inmate. Or perhaps he had escaped. Nobody was really sure. Not even Selina.”
This is taken from the Nuke The Fridge article The Joker’s Whereabouts Discovered During “The Dark Knight Rises”.
No there isn't, and that was an explicit choice by Christopher Nolan given Heath Ledger's death.
Nolan says that "We're not addressing The Joker at all. That is something I felt very strongly about in terms of my relationship with Heath and the experience I went through with him on The Dark Knight".
He added that "I didn't want to in any way try and account for a real-life tragedy. That seemed inappropriate to me. We just have a new set of characters and a continuation of Bruce Wayne's story. Not involving The Joker".
The original intent was to keep their options open on the fate of the Joker in case they wished to use him in The Dark Knight Rises, but Heath's passing resulted in them choosing not to reuse the character.
Heath Ledger's tragedy made it more appropriate to leave the Joker out of the third Batman film entirely. I think if events had transpired differently the Joker would have likely been the main villain, broken out of Arkham Asylum and used Bane as an accomplice to progress the events of the third film.
In the comics the Joker was actually the judge in Arkham Asylum, not Crane. The fact they changed that for the film must be out of respect for Heath Ledger.
