We've got our basic setup. Now we need to figure out how we want to end things and build the story around that.
Villain(s): Figuring out who should be the villain is obviously a key part in creating a plot for the movie. I'm honestly not sure who would be best suited as the main villain, but I do know who I do and don't want to see. The series has been grounded in reality so far and should remain so. That eliminates a lot of Batman's most famous villains. Most likely keeping the realism would mean no Mr. Freeze, Poison Ivy, Clayface, Man-bat, or Killer Croc. I say most likely because in some cases there is the potential to be adapted into a realistic form that would fit into this series.
I'm also pretty anti-Catwoman for this movie. No, it's not because of that horrible excuse for a movie starring Halle Berry and I don't have anything against the character. I just feel that this is not the time for her to be introduced. Catwoman has served as a flirtatious love interest for Bruce for a long time. Like I've said before, Bruce just lost the love of his life and I think they should play that up. It really doesn't seem right for a man who has lost someone he cares for so deeply to fall for a burglar in a cat costume so soon afterward. (That's assuming it would take place soon afterward which I think it should and will) He should have made his peace with Rachel's death and be ready to move on by the time he meets Selina. Anyway, Catwoman doesn't pose much of a threat. She would require someone else to serve as the main villain. This franchise has proven that multiple villains can work in a movie. I actually think using two major villains would be a good idea for this, but neither of them should be Catwoman.
So who would I choose? I would really like to see the Riddler. He's such a classic villain and he would make a good follow up to the Joker. Here's how I would do the Riddler. To present a contrast to the wild insanity of the Joker, I would portray him as very calm and collected while still a bit deranged. He has to feel incredibly smart, and not just like some loser with a gimmick. The Riddler wants to play a game with Batman. He's figured out that Bruce Wayne is Batman so he wants to test him and push him to his limits until he breaks. This would work well with the state of despair that Bruce is already in.
For the Riddler's plot I would take inspiration from Die Hard with a Vengeance. Instead of having the Riddler leaving a riddle with a clue about where he's going to steal something from, he would have bombs placed around the city. Batman has to solve the riddles in order to figure out where the bombs are and disarm them. Meanwhile, the Riddler would put Batman in danger of being caught by the police by somehow leading them to his location. The Riddler would only communicate with Batman, and since Batman can't communicate with the police, they wouldn't realize that he's trying to find the bombs. After stopping the bombs, Batman would trace the broadcast signal to some abandoned building where the Riddler is hiding. He would probably have to take down some armed guards to get to the room where the signal is coming from. When he enters the room he finds that the Riddler isn't there. It's a trap. This part could go one of two ways. The doors would lock and he would have to figure out how to escape a bomb, or he would have to escape a building surrounded by the police as a S.W.A.T. team is sent in to apprehend (or kill) him. I'm leaning towards the S.W.A.T. team thing because it would be really cool seeing him use some stealth techniques to take out a full team. Anyway, all of the messing with Batman has just been a distraction from some larger plan he has. Not sure what that is, but it would have to be something better than just robbing a bank. Anyway, Batman uses his detective skills, figures out who the Riddler is and stops him. The Riddler is sent to Arkham, but he doesn't reveal who Batman is because the knowledge is more valuable if he's the only one that knows. He's disappointed that he's been beaten, but impressed by Batman and eager to break out and challenge him again. It's kind of a roughly thought out plot, but I definitely think elements of it could be turned into something very good.
His background and motivation would have to be figured out and there should probably be something better than just putting bombs all over the place. I'm sure there are plenty of possible Riddler plots that are better than mine. The main things I want to emphasize with this version of the Riddler are his intelligence and the scope of the threat that he presents. Below i've included a manip I made of Wentworth Miller as the Riddler. If you've seen him on Prison Break you may have a better idea of my take on the character.
While the Riddler would make a good villain, he really wouldn't be a physical presence for most of the movie. The Joker really wasn't very concerned about whether he lived or died. Even though the Riddler is pretty crazy, he still wants to stay safely away from danger. For the second villain, it would be nice to have someone who isn't afraid to get right in Batman's face. We haven't seen Batman in a real one on one fight so far so this may be the opportunity to put Batman's fighting skill on display. Fighter or no fighter, there are several possible candidates, for the second, more action oriented villain.
Bane can definitely go one on one against Batman. The trouble is, it's hard to determine to what degree to do Bane strength. In the comic books, Bane is ridiculously strong due to the super-steroid Venom. In order to keep things realistic, Bane could not be bigger than a bodybuilder. If his strength is around the upper limits of what is humanly possible, his muscles would have to be huge, decreasing mobility and making the fight scene less interesting. It's a careful balancing act. The best way to do it would be to make him a skillful fighter, who is stronger than Batman, but not too bulky. Bodybuilders are too bulky, but someone the size of WWE guys like Batista or Nathan Jones (not casting choices, just examples of a possible body type) might work well.
Another villain, Hush, is also a decent candidate. His past ties in with Bruce's and he presents an interesting contrast. The problem with Hush is that he seemed like he was Bruce's closest childhood friend from before the death of the Waynes. That position is already occupied by Rachel Dawes in the continuity of the movies. Going back to Bruce's childhood would mean recasting young Bruce and adding an element to Bruce's childhood which wasn't there before. It's not like recasting would be such a big deal, but when movies go back and add details to previously told parts of a story, the new details feel like they've just been forced in instead of a natural part of the story. Take Spider-man 3's "Sandman was the partner of the guy who killed Uncle Ben. He was the guy who really killed him but it was an accident" as an example of how that can turn out badly. I'm not too sure about Hush, but he definitely has potential.
Two other villains who are well liked, but I honestly don't know very well are Deadshot and Black Mask. Deadshot is an expert marksman and assassin while Black Mask is a crime boss. Any of these characters could incorporate elements from some of the others. Bane and Deadshot could be combined seeing as they're both assassins (not sure about Bane in the comics, but I know he was an assassin in the animated series) . Black Mask and Hush seem very similar story wise from what I can tell. Both knew Bruce Wayne during their childhood and ended up having serious issues with their parents. Either one would serve as a good contrast to Bruce.
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