If I had a chance to work on the next Batman film, though I can't wait to see what Nolan has in store for us, this is what I would do.
Since the last film left off with Batman considered the lead suspect in the death of Harvey Dent and after the first two films delved into epic destruction of Gotham, the citizens should be terror-stricken by now. Everyone can remember huge incidents like what happened on 9/11 and where they were on that day, why wouldn't the citizens of Gotham remember the Joker's raid on the city.He was a merciless terrorist who got all that he wanted.
The Joker went to prison leaving Gotham in a high state of panic. This is what has proved successful for Rupert Thorne prevail in his scheming, because after all he was the one who was actually the true schemer. He was the one who really was employing the Joker, unknown to The Joker. Sal Maroni was a mere fall guy as the guy on the witness stand professed in the beginning of TDK. He was just the meat on the street. Rupert Thorne was the true brains behind the entire operation, he has always been. He is a business mogul and deals in networking. He is an investor who has ties with several many very reputable and successful businesses, while also he deals in receiving revenue from the street through managing the deals that happen. Falcone from the first film was one of his many fall guys. During TDK he hung back watching along side the citizens of Gotham as The Joker demolished the city and all forms of security. He plans to replace Maroni, but his mob bosses are scared and all are ready to back out of being a part of a huge mob coalition. Thus Thorne decides that he needs another distraction like the Joker to get his plans followed through. He needs to get control back over at Gotham PD and he needs to get control with the government, so he hires a slew of lobbyists, and starts work on building up the next candidate for Mayor of Gotham. His choice becomes Hamilton Hill, who is absolutely terrified by Rupert Thorne but willing to follow his bidding.
Batman, or rather Bruce Wayne, finds himself in a bit of hot water. Its almost impossible working as Batman, thus he unable to spend late nights out in Gotham watching over the city, but he manages as his alter-ego Bruce Wayne to keep in touch with Commissioner Gordon and is working via the internet and a special cell phone Batman has given Gordon to track down the real crime boss. Crime has doubled since the Joker's fall, and some of the people are starting to respect the name of the Joker as if he is a true legend. They say he was the one who drove Batman into madness, that's why he killed Harvey Dent, some even speculate that all along it was the Batman who was the bad guy and the Joker was trying to protect Gotham from him. Bruce is trying to enjoy his life back at a newly restored Wayne Manor and dealing with the financial struggles in his company and not having to layoff a single employee. Wayne Enterprises is the only company at the time that is able to say so. Meanwhile in the newly restored and remodeled batcave, Bruce checks his hidden Joker camera to find the criminal still locked up in his cell twitching. He wonders where Alfred is.
Fox pulls a fast one and swoops in and takes Alfred's second knight. Says that knights shouldn't be played as pawns. Alfred says well if he got to retire too he would spend all of his days analyzing the game of chess. Fox reminds him that the option was granted to both of them at the same time, Fox was the only one who took it and actually is starting to miss working, but he is loving his retirement package that allows him to visit just about anywhere in the world that he wants. He wonders if he should go back to Hong Kong, he actually enjoyed his short stay there under Batty Bruce's employment.
Edward Nygma is in a world of hurt too. He is found out to be the cyber hacker who shut down all of Gotham's computer systems for over 24 hours, giving the citizens a "holiday." He is not found out by the police, but by the unknown Rupert Thorne, who is pissed because he lost a lot of money in his legal investments in that 27 hours. Nygma is the perfect thing that Thorne needs in order to take back the city, a distraction. He is the next Joker. However, Nygma doesn't agree, if Thorne wanted the Joker he would free the Joker from his cell in Arkham. Which is only too true, seeing the Joker in action, Thorne realized he needed a madman under his thumb not one that's ready to torch any thing living or not in site. The Joker was too wild, and ready to destroy everything. He has invested a lot of power in order to make sure that the Joker never sees the light of day again. However he has also realized that he has seen a whole host of profits from the happenings, so he informs Nygma that he needs a madman to recreate Gotham in Thorne's own image, that way he can make a much higher profit off of it. Nygma is forced into doing Thorne's bidding. Thorne's cronies have investigated into Nygma's history very much, only to find very little, but enough to create this personality of Nygma's. They find out that Nygma has almost an unhealthy appetite for riddles and puzzles. So they create two names for him and give him a silly one piece costume that is a throwback to the old 60s TV show. The names are the Puzzler or the Riddler. He is forced to do this or either death or imprisonment were likely to come his way, and if he does it well, Thorne might make Nygma a very rich man.
Bad times are in for Commissioner Gordon. He still feels entirely responsible for losing Gotham's White Light and has had to deal with treating his friend Batman as a fugitive, disillusioned still by the whole experience. Crime has risen since the terrorist The Joker was imprisoned and not executed. The citizens are in a state of panic and are not satisfied with P.D.s role in the happenings. There is utter investigation in all departments as to the accounts of what went wrong that left the DA dead, and the killer right under Gordon's nose and yet still he was unable to apprehend the vigilante fugitive known as the Batman.
The Mayor is up for election and can sense the bad feelings against him. Though he still has support from half of the city he decides that he needs the Batman apprehended at once in order to save his political career. But politics is not the game that Gordon likes to play, he deals with crime and trying to stop it. If he brings Batman in, he loses a very important informant and a friend outside of the force. He is the only one that knows that Batman didn't kill Harvey, other then his family, yet he has to deal with letting the lie live and play the political role he never wanted to be a part of. He starts drinking much like the Commissioner before him and has to deal with a new police force in his department, as much of the other deputies were in some way or form involved with the mob. He has not much clue what to do and almost little power and Batman seems to be his only direction in the darkness he is stuck in. Yet Batman can't even appear to him face to face. Gordon is falling into a pit of isolation and depression, all the while his wife tells him not to drink.
Selena Kyle is a young entrepreneur trying to better herself. She is alarmingly attractive and very seductive. Bruce meets her at a party at his newly and finally finished Wayne Manor. She slips in unnoticed to view one of the cities most influential people, only to find the man she meets is more mysterious then she suspects. He is initially uninterested in her thinking that she is merely another woman after his wealth, though she is rather beautiful, only to find that she is a two-bit thief who slips a major artifact from his collection into her coat and tries to skip out on the party early. She seems smooth, but not smooth enough to Bruce who catches her by the arm before she can escape. She hisses at him at first. He is attracted to her in a different manner after they discuss why she was stealing from him and what the piece is worth to him. He wishes that he could give it to her, but it is the last remaining piece of a set of heirlooms that his father once owned the other collection which was lost in the fire of Wayne Manor.
Alfred is trying to help Bruce be chipper in the middle of all of this, by helping him host a slew of parties and rallies to help promote the mayor's reelection, however much of the business owners are not too convinced that their current mayor should even be eligible for mayor for all that happened with the Joker incidents. Bruce learns later that the mayor is really working to expose the Batman and capture him, thus Bruce himself starts to question supporting Mayor Anthony Garcia. Alfred is still working on helping things get back to normal for Bruce and has to deal with the anxiety that Bruce is having on not being able to go out and bring the city's criminals to their knees. Alfred thinks that it is entirely much safer for Batman to stay put away for awhile until he can get his own redemption, he believes that the time is coming when the city will call for him.
Nygma eventually gives in and dons the tights and sets up a scheme to hold an entire five city blocks hostage by a mere riddle alone. If the city can figure out the riddle then no one will get hurt, but however they only have a little time to figure it out.