My Predictions for The Dark Knight Rises based on facts we know right now.

What do we know?
There was an interview with Wally Pfister that I read on here that had him saying he read what Nolan has written after watching Batman Begins and The Dark Knight and he said that he was impressed because they have the “perfect trilogy.” For something to be a “perfect” movie trilogy and not just a third movie it needs something to tie the first film to the second and continue its own story also.

Batman Begins:
3 comic book villains: Scarecrow, Zsasz (small cameo), and Ra’s Al Ghul. 1 comic book mob boss: Carmine Falcone
Inspired by Year one, which was the origin of Batman, featured Gordon as a LT. and not yet commissioner. The film followed this while, of course, adding more to make it more cinematic. The film had bats being trained by Ra’s Al Ghul who mentions that he “wasn’t always in the mountains” and once had a family. He also says that the League of Shadows has been around for centuries and have attacked Gotham before using various tactics such as economics. They used the fear toxin this time and planned to use it like a plague.

The Dark Knight:
3 comic book villains: The Joker, Scarecrow (small cameo), and Two Face
Inspired by The Long Halloween, which is a take on the origin of Two Face. In the film we witness Harvey Dent as D.A. before he finally becomes Two Face. The Joker is a criminal with no known origin who wants to simply cause chaos in Gotham and to “Watch the world burn.” Gordon gets promoted and Batman is viewed as a killer and criminal in the end. There is almost no mention of the events in BB.
The Dark Knight Rises:
Before any major characters were revealed we only knew that Tom Hardy was cast and that Nolan was casting for TWO female roles, one being a villain and one being a love interest for Bruce Wayne. It was revealed after a while that Tom Hardy would be Bane and Anne Hathaway is Selina Kyle/ Catwoman which leaves 1 female role open. Marion Cotillard has been rumored to be cast.

Using these facts here is how I think TDKR will go.

First off the inspiration, Many people speculate it will be Knightfall, and others speculate it will be Prey. I think it will be neither, I personally think the insiration will be Legacy. The plot of Legacy sees Batman joining forces with Catwoman, among others, to find a cure for a plague in Gotham created by Ra’s al Ghul. They encounter Ra’s and his new ally, Bane and Ra’s is still searching for a suitor for Talia.

So for the movie plot:
I think traces of the fear toxin will remain be it in the Narrows, or somehow the trace amounts left in the water supply make citizens sick in an unforeseen way and Batman will have to go back to the former temple of the League of Shadows to find a “blue flower” he can take back with him to research and look for a cure. While there he is shocked to discover the League is still together, the temple rebuilt, and they have a new leader who is plotting to avenge the death of their fallen leader and finish the job of destroying Gotham once and for all. The new leader is Bane and since the death of Ra’s, Bane has devoted himself to destroying Bruce Wayne/Batman but leaving him alive and helpless to watch his city fall. In the first act Bane will injure bats badly but leave him alive. Bats will escape and have to undergo physical therapy in order to regain his physical movement. Luscious will examine the blue flower, and Bruce Wayne will become fascinated with Selina Kyle. In Batman’s momentary absence someone else will put on a costume and call herself Catwoman, she will have good intentions of stopping crime, but steals from the criminals to fund her operation. Once he feels well enough to don the batsuit again, Batman will seek out Catwoman and form an alliance to stop the League of Shadows once and for all.
The two will go overseas and Bane, the League, and a woman who is set on pure revenge for the death of her father, Talia. It is here that origins are revealed. Bane will explain that after Bruce left the League, Ra’s found him in a prison just as he did Bruce. Also like Bruce he became Ra’s best student and was set up to take Ra’s place when the time was right. He wasn’t with them in Gotham because Ra’s wanted to lead the team himself and tie up the loose end that was Bruce Wayne/Batman. Once Ra’s was killed, Bane took his place as leader of the League of Shadows. Talia explains that her father always wanted her to marry the man that would replace him and that it was first to be Bruce, but before she could meet him he “betrayed” the League and left. She has now joined Bane as both his wife, and co leader of the League of Shadows.
Let me know how you feel about these predictions.