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That was pretty well explained in the "You complete me" scene.
So, here's how it laid out. First, the Joker was just robbing the mob because he could. Then he realized the mob was afraid of Batman ("I know why you hold your meetings in the daylight" remember?), and so he tried to negotiate a fee to kill Batman ("If you are good at something, don't do it for free"). The mob split over this, and one of the leaders put a price on the Joker's head, so the Joker killed him, and then the Russian dude and Eric Roberts decided that the Joker could get things done, and allied with him. But by then, Batman had captured the mob's banker and the banker had turned on the mob and gotten most of them arrested, so the Joker had to get the mob out of jail, so he went after the judge, the commissioner, and the DA, and in the process he developed a plan to get the banker out of jail.
By this point the Joker's motives are hard to read because the Joker is playing all sides against each other. The mob believes he is trying to kill the banker in jail to get rid of the witness, and trying to kill Dent and the Batman to get rid of the mob's problems. Batman thinks he is trying to kill him, since he has publicly tried to pressure Batman into giving himself up to the Joker. The Russian mobster thinks the Joker is trying to take over the mob, and allies with him, only to discover that the Joker is just trying to take over the mob. The Joker tells the Russian he just wants to prove that everything burns, and when he goes through the elaborate ruse to wind up in jail, he tells Batman the same thing, and then tells Batman that he has to choose between Rachel and Dent. The Joker claims this is all part of his nihilistic goals, to create chaos and to make the Batman break his own one rule (not killing people).
However, it's never clear what the Joker wants. His wild goose chase ends in Rachel's death and Dent's breakdown, but it also gets Batman and all the decent cops out of the jail so that the Joker can kidnap the banker, so he still seems to be working for the mob, and it's hard to tell whether the Joker's criminal ambitions or his nihilism is his main force. The Joker lies to and plays everyone, even while telling people he isn't lying to them. He uses chaos to divert attention away from him just as the cops are closing in, so either motivation could be driving the other.
That's when he burns the money and the banker and kills the Russian mobster, then breaks Harvey's mind. Eric Roberts has told the cops where to find the Joker, because even he is afraid of him, but just as the cops close in on the warehouse, the Joker calls the media and threatens to blow up a hospital unless someone kills Mr. Reese, who is about to expose the Batman and give the Joker what he at first said he wanted. This diverts the police, creating chaos, and once again getting the Joker out of trouble.
The final two situations--the panic on the ferries and the final snapping of Dent's mind--seem to finally conclude that the real goal of the Joker has become creating panic and chaos, and the final scene of the Joker dangling from a wire demonstrates this. It also shows Batman refusing to break his one rule by saving the Joker, and it affirms his faith in the people of Gotham, so Batman seems to have defeated the Joker in all his possible schemes, until the results of Harvey Dent's insanity becomes obvious. Batman kills Dent--finally breaking his rule, though not completely, since it was self-defense--and then to prevent all of Dent's work being undone by Dent's clear insanity, Batman takes the blame for the deaths and lets Harvey die a hero.
It's a complicated plot which makes complete internal sense even if it takes a couple of viewings to figure out all the angles. We're so used to single-message scripts with plots created for nothing more than car chases or explosions or gratuitous and unrealistic sex scenes that it's hard to follow a genuine plot when we encounter one.
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