Using 'Prey' is a perfect choice, but I'd love to see it combined with elements of 'Knightfall' and other parts of the backstories of Hugo Strange (the primary villain), Bane (the secondary villain), and Catwoman (the love interest/villainess/anti-heroine). Bane would be played by Tommy "Tiny" Lister; the prisoner on the ferry who tossed the detonator out the window in 'The Dark Knight.'
Like 'Prey,' the movie would open with a police sting operation, only this time instead of a drug dealer it's to catch a female thief that goes by the alias Catwoman who's been stealing from corporations around Gotham. The sting is lead by Capt. Stephens (the officer Joker took hostage at GCPD in 'TDK'), the new head of the Major Crimes Unit now that Gordon has been promoted. Bruce Wayne has allowed the police to set up the sting at Wayne Enterprises, attracting her with the prospect of a major score which they announced in the news. However, when she outsmarts the police and steals the item anyway, Batman (who was watching from a distance so as not to get caught by the police) goes after her. He catches up to her, but she's as skilled as he is and doesn't allow him to get close enough to catch her. At a stalemate, Batman switches tactics and tries to talk to her. She tells him the reason that she is stealing from the corporations is that she needs the money to finance experimental treatments for her sick brother. Sympathetic, Batman decides to let her go, much to her surprise. Capt. Stephens witnesses this, and is further outraged by the Batman, who he was already after for the murder of the officers that was actually committed by Dent/Two-Face.
The thief, Selina Kyle; illegitimate daughter of Carmine Falcone, takes her prize to Dr. Hugo Strange, researcher and chief psychologist at Gotham Prison and Arkham Asylum following the arrest of Dr. Crane. She's been financing his illegal experiments to cure her half-brother's (who's in the prison hospital for working for the mob) cerebral palsy ever since his previous benefactor and the young man's father Falcone lost his criminal empire. Unbeknownst to her however, he's been testing his muscle and motor control enhancing drug (called Venom) on a healthy inmate, giving him enormous strength, speed, and dexterity (this is similar to both the "Monster Men" in Strange's backstory and Bane's origin). That inmate is the extremely intelligent mob enforcer from the ferry incident, known in the mob as Bane; a product of the prison system since his upbringing in the Caribbean. He shares his suspicions with Dr. Strange about the identity of the Batman and his desire for revenge against him for getting him thrown in prison again. Strange and Bane form a profile of Batman and determine that he must be extremely wealthy, have access to off-the-books military hardware, and that he's driven by a traumatic experience from his childhood.
This puts Bruce Wayne at the top of their list of suspects, and they hatch a plan to wear Batman out. To do this, Strange offers his services to the Gotham Police as a profiler of the Batman, and Bane stages a massive riot and escape from the prison and the adjoining Arkham Asylum, unleashing even more of the worst Freaks upon Gotham. Batman is forced to operate nearly nonstop taking down the newly released criminals while avoiding the ever tightening GCPD noose led by Strange and Stephens, and gets progressively weaker and more injured. His relationship with Alfred is also strained when he refuses to rest or seek out allies to help him. Strange doesn't actually reveal Batman's identity to the police, since he doesn't want him caught, he wants him worn down so Bane can kill him, thus allowing Strange; who has become obsessed with the Batman during his profiling of him, to take his place. It's learned that Strange was also behind the rash of Batman imitators in 'TDK,' who were mostly patients of his.
When Batman is at his weakest, Bane faces him in the new Batcave while Strange watches. After an epic battle, Bane breaks Batman's back over his knee. Bane throws Batman off a cliff into the water, but Catwoman (who was tracking Strange to keep an eye on his activities) secretly rescues Batman in repayment for letting her go earlier. However, Bane thinks he drowned since he couldn't swim with his back broken. She takes Batman first to Alfred in the new mansion and then together to Falcone's underworld doctor (her mother) for surgery to repair his back and rehabilitation. Her mother will keep Batman's identity a secret. While helping him return to fighting condition, Bruce and Selina's attraction to each other grows stronger.
Meanwhile, Strange, seeing his opportunity following the real Batman's "death," takes up the mantle of the Bat (this is similar to Azrael in 'Knightfall') using a refined version of the Venom drug to boost his strength and speed (but not as strong as Bane, who has to have a constant stream of the drug). He is a much more violent Batman however, not hesitating to use guns and publicly kill the occasional criminals for show (while not actually preventing crime so he still has a job) or the police officers pursuing him as Batman alike. With Bruce out of commission for months during his rehabilitation and the Mob equally broken, the Freaks are able to gain even more control over Gotham. The people are living in endless terror both of the Freaks and of this deadlier Batman in the wake of the Two-Face/Batman's police killings and Strange's behavior as Batman. They've come back around to the idea of needing a hero again.
Selina suspects that the new Batman is Strange, and goes to confront him. In retaliation, he kills her brother, and she vows revenge. She no longer has a reason to be a thief, and pledges to join Bruce in fighting Strange and Bane. They confront them in an epic battle on the streets of Gotham, with the media filming the fight. The police and the whole of Gotham are able to see the alternate Batman fighting alongside Strange and realize that the Two-Face police murders must have actually been committed by this impostor Batman instead of the real deal. Selina kills Strange against Bruce's wishes, and Bane falls during his fight with Batman and lapses into a coma.
Afterward, Bruce realizes that he can no longer afford to work alone, but he can't work with Selina due to her willingness to kill to seek justice. He decides to seek out a new partner soon, someone young whom he can train. He does continue his relationship with Selina however, and she continues her new crimefighting crusade, only on her own. Now back in the good graces of the police and the people of Gotham, and with the Batcave and mansion rebuilt, Batman returns to defending the city with Commissioner Gordon's help.