Here's my story:
The Riddler is the main villian. In my version he is a Detective named Edward(making him a d:ck). He is now called upon more often then before because Batman doesn't come out as often as he used to thanks to his new public image. He doesn't like Batman because he detests vigilantees.
Meanwhile Roman Sions is fired from his subsided company by Bruce Wayne and builds an obvious hatred for him. He is fired because of a make-up catastrophy that he is responsible for.
Selina Kyle, daughter of deceased father Maronni, meets Oswald Cobblepots (Penguin). He has taken over the mafia business and decides that its finally time to come out of hiding thanks to Batman's absence. He plans on smuggling drugs from Japan through a Wayne enterprise port ship. The drug is the notorious 'fear toxin' and he plans on using it to stop the police force and take over Gotham city (He learned this when he visited Johnathon Crane at Arkam when discussing the drug).
Selina goes to tell Bruce Wayne himself (building her justice type character and a romantic tension between her and Bruce). Bruce tells Commisioner Gordon that he thinks there will be illegal activity at his shipping port and he wants extra security there. Gordon goes with a squad of his cops. Edward also wants to go, just to see how it turns out.
Roman Sion goes by the Narrows and pays 5 thugs to go with him to sabotauge the next shipping boat made by Wayne Enterprise (not aware of Penguins activities there). These men belong to the Penguin, but they don't know anything about the drug smuggling also happening. They all go wearing Rubber masks ordered by Roman. Penguin's men arrive there and begin there smuggling, but are then shot down by Roman and his contracted men. Gordon and Edward hear the shooting so they go inside the ship with guns ready.
Roman and the others begin to place the causmetic explosions when Roman hears the cops. He grabs a set of explosions and places them at an entrance where he expects the cops to go by. He then goes back to where he was. Gordon then sends a squad to investigate an area. Edward tells him not to send them there but Gordon doesn't listen. Sure enough a bomb explodes killing off the squad. Gordon is in shock. Edward proceeds through another entrance, insulted by the Commisioner's ignorance. Suddenly one of the thugs is pulled away into a dark corner and Roman's group become alert. They are then jumped by Batman and beaten. Roman sneaks off, but is confronted by Edward at gun point in a corridor. Roman tells Edward that Batman is in the other room. Edward decides to take the law into his own hands and plays a little game with Batman. He ties Roman up in a chair strapped to a bomb. He dares Batman to try to save him. Edward goes off far away to watch, ready to press the trigger to blow the bomb. He is then confronted by a mysterious woman in a black costume. Edward points his gun and asks who's there? The woman pulls a whip and snags the gun out of his hand. She is not fully seen and is mostly covered in shadows (pursumably the Catwoman). This gives Batman enough time to save Roman but just when they get out of the room. Edward successfully pushed the trigger to blow the bomb setting a chain reaction and blowing up the other bombs, which ultimately destroyed the entire ship. Batman covers Roman with his flame retardant cape (learning from the Harvey catastrophy) and is consumed by the flames. Unfortunately the heat itself melted the black rubber mask and it become unremovable. Roman fainted.
So that it my basic set-up. Catwoman gets away and begins to steal more equipment from Wayne's military section. Gordon suspects Edward died in the bombing of the ship and is pronounced dead to the public. Roman is left at the hospital, but his Black mask becomes perminant, pressing against Roman's face to the point where his teeth were revealed and made it seem as if he had no lips. Edward becomes insulted by the police forces idiocy and decides to go under a new name and test Gotham's intelligence, going by The Riddler. Under this new enigma he will make people hate Batman and frame him for more deaths than just 'Harvey Dent's'.
Black Mask sees a photo of Edward that says he is dead, but he believes undoubtedly that Edward is the Riddler based on his sinister actions. He escapes the hospital and goes on a hunt for Edward, then Batman. Catwoman steals Wayne Entreprises's Military armory (where Batman gets his) and continually upgrades her Catwoman costume. Her goal is to stop Penguin's activities as much as she can while getting the most jewelry for herself. Penguin is trying to bring back the power to the mob and eventually hires Black Mask to take out the Batman and Catwoman. Batman of coarse, has to stop everyone. Bruce Wayne has to keep his public image as the party playboy billionaire and restore a new love as he goes as with Selina Kyle after they're first conversation.