I thought of a good put-together plot based on various other theories going around the board, which is long shot because it involves the Lazarus Pit.
Ras al Ghul, resurrected by a Lazarus Pit, and recuperated during the events of TDK, will see the change in Gotham and will acknowledge Bruce's transformation into a true symbol (instead of looking at it mockingly and derisively as he did in Begins, he will show it some respect), but Bruce must be tested once and for all. Talia will act as Bruce's love interest and will test him secretly to test once and for all if his crusade is good to prove to Ras he is worthy and Gotham is as well, and that Bruce can save Gotham. One possible way he could prove this is by fulfilling Ras' speech in Begins about becoming a legend and rising above and overcome his trials and become more than a man. Talia will fall for him.
Black Mask has taken over Gothams mobs and the underworld but is not necessarily a major player in the story; he might have a role equivalent to Maroni in the first movie, but not the main villain, which will be the bounty hunter. He might possibly hire the bounty hunter in order to collect on the bounty and finally prove himself to the mob for good that he can lead them as he is the man who brought down Batman.
Tom Hardy will play Bane or Slade and will hunt Batman down and finally kill him against orders to only capture him alive. His death will either be in circumstances proving his worth to Ras (the least likely scenario), or Talia will collect his body against Ras orders and will take Bruce to a Lazarus Pit and resurrect him, at which point two things could happen.
1. Ras deems Bruce worthy for whatever reason: The people and police on hearing of Batman's death feel that they have gone too far, and the killer is hunted. Ras brings Bruce to the Pit himself and Bruce heads back out to catch his killer and to face them down once again, this time ready for them.
2. Talia saves Bruce with the Pit/Batman was wanted Dead or Alive: Bane/Deadshot/Slade has killed Batman against orders and he is being hunted. Ras will deem Bruce unworthy and Bruce will have take drastic measures to prove himself and Gotham or Ras will destroy it once and for all and Batman will not be able to stop him. He must do this by capturing his killer and proving himself to the people once and for all he that he is a legend and is more than a man because he came back from the dead. Ras will not destroy Gotham and will leave it in Bruce's hands.
Also, instead of resurrecting someone, the Pit could heal them of their injuries and have more rejuvenating powers, so while everyone could believe Batman was killed, he could have just had his back broken (by Bane) or been severely almost mortally injured (by Slade). Similarly, Ras could have been almost mortally injured and crippled by the train crash but could have been rejuvenated by the Pit. Rejuvenating powers and the mysticism of that might be a more grounded concept that I could see Nolan doing more than resurrection.
Now I look forward to seeing how Nolan does something completely different than this and blowing my expectations and mind wide open.
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