I have updated the story synopsis below based on last week’s spy reports and some informed speculation from this thread, as well as by yours truly.
In the wake of the events of the first film, and Falcone’s incapacitation, there is now a turf war in Gotham between rival gangs. Sal Maroni is heading the Falcone family, Scarecrow is heading his own gang, there is a Chechnyan group, and then a final gang headed by a thug called Gamble. There might be others, too. As the film starts off, Scarecrow and his thugs are about to close a drug deal, possibly involving an improved version of the toxin from the first film, with some members of the Chechen gang at a car park. The Police get a hold of this, but are unable to intervene because they are thin on the ground due to the sheer number of violent cases that has Gotham in its grips. The Batsignal is turned on, and we see Bruce Wayne, living in a downtown penthouse while the Wayne Manor is buing rebuilt, react to it. He presses a few buttons on the wall, turns a screw or two, and goes inside a trapdoor to don his new Bat-costume. I have a feeling this is also where we will meet Alfred for the first time – with perhaps a quip from the ever loyal butler.
When we cut back to the drug deal between Scarecrow and the Chechens, we see that things have already started turning sour. There might be some threats to and fro between the two gangs, and there might be talk of a traitor or an inside man: I am basing this speculation on the carpark filming clip where that guy who thrown onto the ground in front of the Scarecrow. Anyway, the thugs hear something - the thunderous roar of the batmobile as it demolishes the far end of the carpark – and they quickly scramble. Those that stay behind fire at the Tumbler, only to find out that Batman is not even in there when he ambushes them from behind (not like that, you perverts). Meanwhile, Scarecrow shuffles to the van and tries to make a quick get away. Batman jumps on the van and tries to get Scarecrow out of the van as it spirals down the car park. Eventually, he does, and Scarecrow is apprehended.
There is a also new major villain on the loose who calls himself The Joker, who is unrelated to any of the rival gangs. Fairly early on in the movie, he and his cronies pull off a major bank heist which involves driving a school bus into the building, and ends with the shooting dead of the bank manager. Joker does not leave the scene right away; he has a chat with the bank manager before he kills him, who says that the Joker doesn’t know who he is working for. This might end up being Sal Maroni, but I think the Joker will be aware of this and we, as the audience, will only come to realise that he was in cahoots with the Maroni gang (or some other organisation) near the end of teh flick. It is also my feeling that he does not make his get away straight away because he wants Batman to make an appearance. With the police and a SWAT team surrounding the bank, and with the bank personnel and the customers as his hostage, Joker bides his time, until Batman intercepts the event. There is a chase scene, that might involve the Batmobile or even the Batpod, yet the Joker manages to get away. There is a chance the Joker might get injured during this action scene, but I, personally, don’t buy it. I also don’t think this will be a flashback. The film seems to be tightly packed and very fast paced: the immediacy and the urgency of the situation at hand does not leave any room for leisurely flashbacks as in the previous film. Again, that’s my personal opinion.
Meanwhile, there is a new district attorney called Harvey Dent who might or might not be going out with Rachel Dawes. Like his predecessor before him, he is trying to bring to justice a Gotham crime lord called Sal Maroni, and he is in a clandestine league with Batman and Jim Gordon to do so. His alliance with Batman is tested during at least one scene on the rooftop with the Batsignal where the two meet, and this might very well be the scene where Gordon and Bats discuss whom to go after: the gangs or The Joker. I think Harvey Dent will think it more pressing to go after the gangs. At one point, all the major gang members, including their leaders, are apprehended and are taken to court. Sal Maronis is there, too. Now there are two ways this can work: either Sal Maroni scars Dent in this scene, or later, possibly, when Dent goes to talk to Maroni behind bars. Either way, I think one of the corrupt police officers will let someone slip the acid to Maroni, and it is this very officer whom Dent/Two-Face kills at the end of the film.
We are still not clear about the Joker's true intentions. However, his homicidal nature is complemented, as in his first comic book appearance, with a lust for cash or jewels or whatever it is he's trying to get his hands on. I have a feeling that his apparent psychosis will, at least initially, be a cover to his larger ambitions to steal a huge amount of loot of some sorts (kind of like Hans Gruber in Die Hard). At one point in the film, he probably comes into contact with the Scarecrow (if that is indeed him on that footage - and it seems likely). It seems logical that he works with the Scarecrow, if only briefly maybe, to fashion his laugh toxin. One of the major set pieces includes a lively parade through Gotham (which will be filmed in Chicago in August). It is reasonable to assume that Joker will make an appearance of sorts. Maybe a Joker balloon releasing the Joker toxin as an homage? I doubt it, but the Joker will be there in one way, shape or form.
Bruce Wayne will also be up to his usual playboy shenanigans - during one interlude, having a Bolshoi ballet performance cancelled when he holds a party on his boat for the cast. He also holds a party at his penthouse for Gotham's glitterati, which is crashed by The Joker and his thugs. The Joker asks for Batman to reveal himself, which is when Harvey Dent falsely claims that he is Batman (I am Spartacus), only to be hidden in a closet by Bruce Wayne, who summarily makes an appearance as his alter-ego. A fracas ensues, and it is safe to say that the Joker, once again, manages to get away.
The Joker's piece de resistance, and the film's finale, seems to involve his threatening Gotham in a way that involves, possibly, the releasing to the air of his toxin. There is a mass exodus from the city inviolving two boats, one full of criminals (and, possibly, the general populace of the Narrows), and the other full of Gotham's more affluent denizens. The Joker claims both boats are rigged with explosives, and dares the authorities to blow up one boat, lest they want him to destroy both. We won't know the outcome, but the final confrontation with Batman seems to be set against this tense backdrop.
Of course, there are huge gaps here. Sal Maroni's role in the proceedings; what Jim Gordon gets up to; what about Alfred or Rachel, etc., etc. Feel free to fill in the missing pieces.