Ok, my basic plot outline:
Sal Maroni and Rupert Thorne have moved into Gotham after the demise of Carmine Falcone. Both are a little hesitant though to take over Gotham after hearing stories and tall tales about a mysterious Bat-creature, half-man and half-bat that terrorizes the skies and the streets.
However, both are fighting for territory and turf like two pitbulls over a scrap of meat. They're both being funded by a British armsdealer named Oswald Cobblepot who is a short, stout, and pudgy man who waddles and quacks like a penguin. He also has webbed-hands and a bird-like nose, whom if anyone stares at his sightly features, he'll shoot them dead in his tracks with his semi-automatic umbrella. Little does the Maronis and Thornes know Penguin's intentions and loyalty lie with someone else...a man whom has driven Batman "batty" for months now.
Gordon is near-shy to closing the case of The Joker, but Batman tells him again and again he'll find him no matter what.
We get a backstory explanation of how Joker came to be, but he mostly lies hidden the shadows, along with Penguin like how the villains were portrayed in "Begins."
Sal Maroni and Rupert Thorne and their rivalry are concentrated on alot more.
While all this is going on... Bruce Wayne is trying to reestablish his company with his friend Lucius Fox. Rachel Dawes has moved on and out of his life and a new D.A. has come to Gotham City, named Harvey Dent, who plans to clean up Gotham City once and for all, with or without a Batman to help him.
See, when we meet Dent I believe like Gordon was in "Begins" he'll be skeptical of aligning himself with a masked vigilante. Till movie's end he'll definitely align himself with Batman and him, Gordon, and Batman will carry on a long-lived partnership till movie 3 where Dent is sprayed in the face and becomes Two-Face.
I like alot of what kytrigger had, but I think this part he wrote about: " Meanwhile, Bruce is so pre-occupied with all the things he has to do as Batman that he almost completely neglects his duties at Wayne Enterprises. Instead of going in to work, he just goes back down to the cave to investigate some more. ALfred starts notcing that when he is in teh cave, he is almost a completely different person, and that persona is starting to show in teh manor as well. Alfred tries to remind Batman that Bruce is just as big a part of his life as Batman is, but Bruce waves him off. Fox is covering for Bruce at the company, but Earle comes back trying to make a hostile takeover of the company with Roman Sionis backing him."- Works very well.
Along with: I loved the ending you made up, but I think if the Joker were to abuse Dent's wife Gilda, or if he were to torture, rape, and kill Gordon's wife that'd be the one thing to set both of them off and really wanting to take down The Joker any means necessary. If you went with either or storyline, it'd make Batman be tested whether he should bring Joker to justice, beat him to a bloody pulp, or kill the sick twisted bastard.
Later, he'd realize killing him would not be the answer, but a lifetime being held in Arkyum would be a more fitting punishment. Of course by movie 3, he'd get out, and then Dent would come after him for disfiguring his face and for abusing Gilda right in front of his eyes when he could've helped her or saved her.
Now as for other characters in the movie:
-At the end I'd love to see Harley Quinn visiting Joker and then fading to black with her saying, "Aww...puddin' " or something like that.
- Bullock and Montoya would be nice to bring into this movie either with a cameo or not.
-Killer Croc would be a great henchman for Penguin. Think about it both are deformed human beings so it'd make sense with them working together.
-At the end of the film also I'd love to see Batman and Gordon on the rooftop like "Begins" and Gordon telling Batman about a female cat burgular who has a thing for S&M, whips, and latex bodysuits or maybe about a serial killer/mad bomber who loves to leave riddles. If you had that it'd be geektastic.
Anywho...that's my plot idea. You can take it or leave it.