I'd have it centre on Arkham mainly, with a much more gothic feel.
Here is an outline of how I'd end it, it's a bit long
Dr Quinn is observing the case study of famous rogues, we see clips of crimes captured on film- The Penguin giving a speech, Two-Face at the circus and Ivy at the charity event. Finally she watches the clips of the Joker- footage of his poisoning, and of the adverts whereby the models say "Love that Joker". Quinn is hypnotised by him...she repeats it to herself- "Love that Joker".
Professor Crane becomes increasingly aware of her obsessions with the Joker, and offers to help her learn more. He reveals his alter ego, The infamous Scarecrow, to Quinn and pursuades her to aid him in bringing down Batman, whom he feels is a challenge worth taking.
Batman has opened his life up to Julie, whom he has married. The happy time is brief, as she is missing presumed dead from early on. This puts the Dark Knight back into a serious attitude while he investigates her disappearance.
Batgirl is much more independant in this movie- she is more of 'an agent' than a sidekick, and does her own patrolling. She runs into Harley Quinn who is holding up a bank. They fight and Quinn escapes.
Robin doesn't whinge or moan, he's much more adult and mature, and spends a lot of the film concentrating on a villain like Zsasz or someone.
The Scarecrow tires of his prisoner Julie, and kills her before sending the body back to Wayne Manor.
Alfred receives the parcel, Bruce receives the message. The mask goes back on, and the anger that he hasn't felt since Jack Napier terrorised Gotham returns quickly. The Batmobile shoots wrecklessly towards the City and he makes the criminals truely fear him. Batgirl learns of the Scarecrows true identity through her computing skills, and works out that he and Julie went to school together, where she teased him for him appearance. Batman heads to Arkham, but it's a trap. (Nameless) inmates are set free and make it hell.
Harley Quinn declares her crimes in the name of the Joker, hoping to attract attention. Batgirl goes to investigate, and begins her final fight.
Zsasz is finally cornered by Robin, and they have a spectacular fight where Dick is slashed, but ultimately defeats him. Detectives Bullock and Montoya, accompanied by Officers, arrive on the scene to take him away.
The Scarecrow breaks into Police headquarters and sets off explosives which spray out fear gas, sending the police force into chaos. Commissioner Gordon, and others, make it to the roof to use the Signal. Bullock is contacted too, with Robin beside him. The Redbird and Police Cars speed to HQ in a hurry.
The scene is filled with chaos, Robin manages to rescue Gordon and the others, then hears Batman's bleep for help. Gordon calls for backup to control the crazed police and tells Robin not to hang around if batman needs him. Harley lures Batgirl to Arkham, where she surprises her and shoots her in the spine.
Batman defeats the inmates, and comes up against the Scarecrow. Robin arrives too, and Crane uses his fear gas on him, leaving him vulnerable to his gang and their attacks. Batman goes after the man himself and ends up hallucinating about his parents, their death and the Joker's tourments.
He sees the Joker laughing constantly, watches Catwoman fade into the dark and vanish, and Harvey Dent crawl on the ground with steam rising from his face.
Then he sees Vicki, Selina, Chase and Julie and brings himself to snap out of it. He defeats Scarecrow and gives him a taste of his own medicine. Bruce rushes to Robin, who is in a critical state, but begins to crawl to Batgirl. Harley Quinn emerges and strikes at the already weakened Batman. She hits with all she has, but is stopped. Once she is handcuffed she breaks free from his hold and takes a leap from Arkham to her death, laughing as she'll be nearer to her puddin'.
Barbara, in a wheelchair, is beside Alfred as they look up to the sky. Batman, who stands over a gargoyle, with a blue-suited Nightwing behind him looks out to Gotham, the city which needs him.
It's very long, I know
