Here's what I think I've put together, in terms of one long action sequence, perhaps in the middle of the film (more on that in a minute):
1. Joker crashes Bruce's party for Dent, clearly aiming at flushing Dent out as Batman (hence threatening Rachel, if the rumors are true.) Batman shows up in the flesh, they fight (perhaps it's one-sided, since Joker has so many armed thugs), and Joker escapes out the window (based on spy reports - maybe or maybe not with Rachel, depending on whose spy reports you read.)
2. The semi chase follows the party scene - ending with Joker confronting the Pod-riding Batman on the streets outside Wayne Tower. Joker is somehow captured - perhaps he goes willingly, as we all suspect.
3. In jail, he's interrogated to no effect, so Batman is brought in - either officially by Gordon, or on his own intent. Clearly, Batman kicks the tar out of Joker, but all for naught - Joker laughs in his face.
4. Joker somehow escapes - many spy reports indicate it's because one of his henchman (or just some random inmate) has a bomb in their stomach, which explodes. In any case, putting together some side information, here's what I think happens: before Joker gets out, he sabotages the police station - he ties up various police officers, kills Loeb (who's there, as we can clearly see in the trailer during Gordon's voice-over with Joker in the holding cell), and steals some cop uniforms. He then escapes in a police cruiser (also seen in the trailer.)
5. Loeb's funeral is held - which Joker crashes dressed as a police officer. He tries to off Mayor Garcia during the 21-gun salute, but fails to kill him...
6. However, in my interpretation, the mayor is badly injured and is taken to the hospital under heavy security. So, rather than try to sneak in and finish the job, Joker elects to just blow the whole dern thing up (also in the trailer.)
Here's where it gets interesting: clearly, if I'm mostly right about these sequences, the semi chase isn't Batman and Joker's final confrontation, since so many things happen afterwards. However, it's also not their FIRST - Batman is clearly wearing his new suit in the party scene (can see this, too, in the trailer) and also drives the Pod during the chase sequence. Rumors hold that Joker causes Batman to change both his suit, and also use the Pod - the ol' reliable info is that Joker blows up the Tumbler, and Batman nearly drowns in the old suit. Whether this is true or not, it's clear they've met before.