Here's what we know, Bane and Catwoman will appear. JGL and Marion Cotillard are in talks to join the cast. The film is shooting in Detroit, New York City, London, Los Angeles, Pittsburgh, and India, perhaps Romania as well (I think that's all of it). After the events of TDK, the GCPD will be hunting down Batman for five murders including Harvey Dent. Now considering all of that, let's speculate shall we...
I think the story will begin with a worn-down Batman on the run from the police. We'll see the new Batcave and a replacement for the tumbler (something sleeker to evade the police). I think the salt mines in Romania would be an excellent choice for the new look of the Batcave.
Bruce will be neglecting his duties at Wayne Enterprises and will be on the edge of quitting being Batman. Lucius Fox will note this and suggest that Bruce give up his nightly exploits for a while. Fox will say something to the effect of how important it is that Bruce maintain the company his father worked so hard to build. I'm thinking we'll see the stuff shot at the NYSE tie into Wayne Enterprises somehow (perhaps stocks taking a big hit on the market).
After this, there will be a few filler scenes and the mentioning of series of break-in's by someone known as "the cat" at Wayne Enterprises. The GCPD will investigate and assume that the cat is working with and helping the vigilante known as Batman.
Around this time the Mayor will ask Gordon to form a task force to capture Batman and all of his accomplices or he'll be out of a job. Batman will be Gordon's primary target, and he is to do everything in his power to bring him in for the deaths of Harvey Dent and five others. Gordon reluctantly agrees and begins searching for team members. He decides to ask a new recruit with a strong head on his shoulders and a hatred of Batman, Sgt. Max Cort. Gordon however, is more concerned with a series of brutal murders that have been hitting Gotham that appear to be mob related.
Bruce decides that Gordon is the only cop in Gotham who he can trust and decides to have a meeting with him at a secret location. Gordon voices his concern over the new task force and the pressure he has been receiving from the Mayor. Batman reluctantly understands but turns his attention to the gap in the mob ring when Maroni was killed by Two-Face. Gordon tells Batman of Alberto Falcone, Carmine Falcone's son, coming to Gotham from studying in Europe to help with his family business. Batman will look into it. The cat burglaries are mentioned but they don't seem to warrant any attention.
Batman tracks down a few members of the old Falcone mob and the members all claim Alberto is dead or still in Europe. Batman asks who controls the new Gotham underground and they claim someone by the name of Black Mask is vying power of all organized crime. As Batman investigates further, he runs into the cat burglar who broke into Wayne Enterprises. Catwoman will say something like, "Nice duds, we must shop at the same store" and fights Batman. During this scene, Sgt. Max Cort and other members of the GCPD task force break in and surround Batman and Catwoman. They both evade capture and Sgt. Cort is left empty handed.
As the film progresses it is revealed that Alberto Falcone is still alive, and has been murdering/torturing women as Black Mask to make a name for himself on the streets. He is in control of almost all the criminal underground and takes Catwoman hostage. Unmaked, Selina Kyle reveals she is actually the illegitimate child of Carmine Falcone and that she deserves to be in control, not Alberto. Alberto/Black Mask finds the claim hard to believe and tortures Selina, leaving her to die. The Batman task force eventually finds Selina almost dead and decide to use her as bait. Black Mask is later apprehended by Batman and left as a "peace offering" to the GCPD.
After an action scene of Batman saving Catwoman and once again evading the task force, Bruce brings Selina to the Batcave to recover. Unknown to them, Max Cort, as Bane, was tracking them the entire time. After watching how Batman handled himself before, Bane quickly overpowers Batman and severely injures his back in the batcave. Bane looks to Selina and claims that she doesn't play a role in things to come. Bane unmasks Batman and takes his cowl as evidence that he's broken the bat. Bane say's he won't turn Wayne in if he gives up being Batman. Bruce reluctantly agrees.
What follows is Sgt. Max Cort taking all the credit for finding and "killing" Batman. He also takes credit for apprehending Black Mask. Bruce is hospitalized and Selina Kyle has disappeared. Alfred gives some sort of inspirational speech and we see an emotional scene of Bruce visiting his parent's grave. Bruce tells Alfred that he's failed and must somehow find a way to reconcile his past demons. Bruce leaves for Asia (perhaps India going off of the filming locations) to seek out a famed martial artist he heard about when he was training with the League of Shadows. Bruce wanders throughout India and finds the mysterious and beautiful Lady Shiva.
Bruce devotes himself to the training of Lady Shiva and wears a training outfit similar to what we saw in Batman #509. Shiva forces Bruce to kill someone unwillingly and claims that he has finished his training and is ready to face whatever challenges await him. She urges Bruce to give up whatever life he had and join her and her exploits. Bruce rejects her offer. Lady Shiva then turns violent and attempts to kill Bruce. It's revealed that Lady Shiva is actually Talia al Ghul, the daughter of Ras al Ghul. It is also revealed that Bane, working within the CGPD under the cover name of Max Cort, is an agent of Talia al Ghul, ordered to defeat Batman and sway Bruce back to the league of shadows. Bruce barely escapes, but he believes Talia has purposefully let him go.
Bruce returns to Gotham. With Batman defeated, Bane (Sgt. Cort) became the new Commissioner of the GCPD and replaced Gordon. Bruce hesitantly takes up the mantle of Batman once again and gets a new suit from Lucius Fox. Batman then seeks the help of Catwoman, believing she can help him find the balance between his two personas.
After hearing of Batman's return to Gotham, Bane kidnaps the mayors daughter and quickly claims Batman is responsible with Talia overseeing the whole process. Batman, with the help of Catwoman, confront Bane and Talia. Talia quickly defeats Catwoman and turns her attention towards Batman. She tells Batman that she set all of this up to avenge her father's death. But when she met Bruce, she fell in love with him. She tells him that she is now conflicted between the love of her father and the love she feels for Bruce.
Bane ignores this and simply wants to kill Batman off once and for all. Batman takes his mask off and trys to reason with Talia, he gives some speech about finding an equilibrium between extremes and that we all need to rise above our personal feelings and do what is right.
Bane fights the mask-less Bruce and Talia pulls out a gun. She points it at Bruce and then at Bane. Catwoman then quickly intervenes and gets shot after killing Talia. Catwoman says something like, "***** doesn't play nice." Catwoman then escapes into the night.
The end of the movie would have Bane apprehended and formally charged with kidnapping the mayors daughter. Batman would remain a criminal in the eyes of some, but in other's he would still be a hero for intervening in the kidnapping. We would hear of a jail break at Arkham Asylum where the Joker has escaped. Bruce realizes that he will always have a role to play as Batman and as the Dark Knight, it is his duty to walk the heroes path. Cue new Batsignal and Batman watching the night sky.