If you didn't like it or if you thought it was anything at all like Usual Supsects, you probably didn't get it.
Everything up to the last twenty minutes is set-up. The key is to concentrate, but not to think too much. You'll either get it or you won't The mastermind was not Danny, it was the assistant DA, "Jackie". She was playing Danny. It's my belief that she was also an FBI agent. She was, as LL's character hinted when he said that even the FBI had been penetrated, the dirty FBI agent.
She was pretending to be black, as she new this would get Danny's attention and make him believe she could be manipulated. She made Danny feel comfortable enough to give her information about rival gangs which she used to propel herself into the DA's office putting her in a perfect spot to manipulate Ray Liotta's character.
LL Cool J was an FBI agent, although he was not dirty. The chief of police was in on the whole deal with Jackie as he was the one who let her out in the end.
Jackie decided not to press charges against Taye diggs' character as to draw suspicion towards him in the end. She also new he would point out anybody as Danny. That was imperative as it set-up LL's character.
She set-up the hit men who wanted Ray's character dead. She pointed Mekhi's character out as Rupert. Rupert was the one who rigged the gas explosion.
After Danny got arrested, everything went on to her.
The key is to remember that the main plot had little to do with Jolene's character being raped, and it had little to do with LL's character.