Here's an idea that's partly taken from No Man's Land. Joker is being transferred via plane from Gotham's Arkham Asylum to a New York Insane Asylum lab to have tests done on him. Joker manages to take control of the plane and turn it all the way to Iran. While there he secures several nuclear bombs. He contacts The White House and tells the President that he is planning to blow up Gotham if they don't declare war on Iran and destroy several oil rigs there. If they refuse, then he'll blow up Gotham with a nuclear bomb, and destroy the oil rigs himself. Either way they'll be in war with Iran and gas will likely go above $10.00 a gallon and then they'll have near about a civil war going on. No oil in America = chaos = Joker. Batman travels to Iran (via Batjet), stops Joker on top of an oil rig and in the process the oil rig explodes. Joker escapes in a helicopter but Batman uses a new and improved grabbler gun which is made to shoot one end of the chain on one object, then the other end on another, then it releases the chain all together allowing both objects to hold each other back. He does this to the helicopter and the oil rig. It brings down the copter and Joker jumps out into the ocean. He then uses his detonator to release the nuclear bombs. Batman gets into the batjet and chases down the nuclear bomb. He neutralizes it within miles from Gotham. It falls into the river beside it and we see a huge water mushroom!
Next part is optional (depending on whether or not Nolan is returning)....
Joker relies on plan B and detonates several large amounts of dynamite throughout the city knocking over a bunch of tall buildings (including Wayne Tower), which in turn falls over crushing more buildings. Lucius Fox is trapped in the bottom of Wayne Tower in the Applied Sciences bunker. He manages to get out. Causalities in Gotham reach an unparalleled level with the terrorist attacks from Joker. This leads to No Man's Land which will be carried out in Batman 4.
This brings into the story three key elements in today's world: Gas prices, nuclear bombs and terrorist attacks. And this, of course, is the final battle. Before it we have Riddler doing all types of shenanigans to trick Batman and the cops over the issue of Batman's identity.