Here's an idea I have been kicking around...
Years after The Dark Knight, the Joker was put away in Arkham and murdered shortly after and Batman has gone underground. Bruce Wayne is working vicariously through his company to help clean up the streets of Gotham. So, Wayne Enterprises begins hiring on more personnel. One of which is Selina Kyle, a young, beautiful and tough woman. She quickly catches Bruce's eye and he decides to try to court her to speed up the healing process from his lost love Rachel. Dr. Jeremiah Arkham has recently taken control of Arkham Asylum from his Uncle Amadeus and has put a plan in motion himself. He believes that all Arkham inmates can become rehabilitated members of society. So, he brings in a doctor the head up this project, Dr. Harleen Quinzel. Dr. Quinzel, though, has a plan of her own. She is obsessed with the Joker and, upon hearing of his murder, decided that she must seek revenge. So, while interviewing inmates, she tries to discover who it was that killed the Joker. The second part of her plan is to kill the person that put the Joker away, Batman. Commissioner Gordon has had a team of his "top" detectives searching for clues as to the identity of the now missing Batman. Since the appearances of Batman have become more and more scarce, the team really has nothing to investigate. Soon, they find that they keep running into a private detective who has been hired by an unknown source. The detective continually becomes a thorn in Gordon's side by continuously searching and not dropping the case. The detective, Edward Nygma, is determined and will not stop until he solves the riddle of who is the Batman? Bruce and Selina continue to date while Dr. Quinzel begins to interview a new patient, Dr. Jonathan Crane. Nygma becomes obsessed with the Batman until he gets to the point of not sleeping and spending every minute trying to put together the clues. Finally, he gives up and snaps. He decides that the only way to find Batman is to draw him out (His financial backer also encourages this train of thought). He takes on the persona of the Riddler and begins a reign of crime on Gotham. His backer gives him support with some criminals from Gotham's underbelly. Bruce takes notice of this new criminal and is torn between stopping the Riddler by becoming Batman again and having the ones he loves get hurt again. During a hypnosis session with Dr. Crane, Dr. Quinzel gets out that Crane was the one who murdered the Joker. Upon hearing this, Dr. Quinzel jabs her pen into Crane's throat and keeps stabbing him uncontrollably. She lets out a high pitched laugh as his blood spatters onto her. She finally stops, stands shakily and turns to find two orderlies standing behind her. Taken off guard, she stares at them shocked. One of them says Dr. Arkham would like to see you, we'll take care of this. This confuses her but she complies. She leaves and heads to Dr. Arkham's office. She gets to Arkham's office and finds it dark with a single light. Arkham is sitting at his desk with his back to her. He tells her that he knew she wasn't here to just be a doctor and that he knows she had a thing for the Joker. He tells her he knows she wants revenge and he believes he can help her. She asks how and he turns to reveal that his face is covered by a black mask. He says he knows who the Batman is and has already set a plan in motion to bring him down. She asks what the plan is. He says he has united all of the crime families, gangs and sindicates and infiltrated major points of importance including Wayne Enterprises and he has a pawn, Riddler, working on bringing Batman out of hiding. He asks if she wants to be partners. She responds by saying call me Harley. Arkham calls Riddler and gives him instructions. Bruce later gets a call from Selina and she is frantic. The Riddler takes over the call and tell Wayne that he wants Batman to meet him and Selina on top of Wayne Tower at midnight. Bruce slams down the phone and suits up. Riddler is holding Selina hostage right at midnight when Batman arrives to Wayne Tower. Riddler releases Selina and attacks Batman. Selina gets to the roof exit and tries to escape while Batman and Riddler fight. Watching from afar, Harley is holding a detonator while Black Mask stands beside her. He tells her that everything should be in place in Wayne Tower, his men finished the day before. Harley gives out a high pitched laugh and pushes the button. Wayne Tower explodes into the Gotham night.
If this were to come to be I think Gotham would be a good name... or 3 guys a girl and a feline. Also, here's who I think would be good in the roles. Scarlett Johansson as Harley, Daniel Day Lewis as Arkham, Ellen Page as Selina Kyle and take your pick for the riddler Joseph Gordon Levitt, Emile Hirsch or Johnny Depp but I'd prefer Levitt. Let me know how terrible this idea is...