Now, I'm just typing this as I think, but here we go.
TDK ends with Batman as a fugitive. Meanwhile, Batman is still doing the whole superhero thing, just working even more in the shadows than before. I can't decide if he should still have secret meetings with Gordon.
So, the cops are looking for him and maybe the mob gets wind of this and they want in on the deal for immunity or getting out of jail time or something. A mob boss--could be made up for the purposes of TDK2 or could be one from the comics (Thorne, Penguin, etc)--could hire someone to find and kill Batman. This hired killer could either be Deadshot or Bane. Anyway, if the mob brings in Bane we could get an abridged storyline from Knightfall. Maybe not have Bane break Batman's back, maybe have him break his leg near the thigh or something. If it's Deadshot, have him shoot Batman in the leg. Whoever causes the damage and whatever the damage is has to get Batman out of the way for part of the movie.
While Batman is in a recovery state, things get even worse in Gotham. Batman is presumed dead and or captured by the police and public, but someone is running around pretending to be Batman. Gordon, wanting to investigate the new Batman, sets up a meeting with him (maybe with a new Batsignal). At the meeting, the fake Batman abducts Gordon. Turns out it was Two-Face (or it could be someone else if Two-Face is dead, which I don't believe) masquerading as Batman. So there is breaking news that Gordon has been kidnapped and Batman goes to save him, in a weak state.
I don't know, I just typed all that really fast, but I think it's one of the possibilities for TDK2.