A robbery homicide investigation triggers a series of events that will cause a corrupt LAPD officer to question his tactics.
Set in Los Angeles, following a few officers in the Los Angeles Police Department in April 1992, Dark Blue takes place from a few days before to during the acquittal of four officers in the beating of black motorist Rodney King and the subsequent L.A. riots. The movie begins with some of the footage of the Rodney King beatings and then switches to a scene showing Sergeant Eldon Perry (Kurt Russell) pacing around in a motel room. He grabs a shotgun and pistol, and then the movie cuts to a scene with two men in a car, five days earlier. The two men, Darryl Orchard (Kurupt) and Gary Sidwell (Dash Mihok), appear to be robbing a convenience store, when they are actually after a safe in the room above the store. In the process, four people are murdered, and one severely wounded. The story then shifts to Detective Bobby Keough (Scott Speedman), who is in a Gun Board hearing in relation to an application of deadly force. His partner, Perry, defends him, and the two leave.
Perry, Keough, and Jack Van Meter are all sitting in a room when they find out that Keough is exonerated. Jack Van Meter is Keough and Perry's superior and a man of poor moral character—he often has his subordinates fabricate stories and evidence. It is later discovered that Perry killed the man that the Gun Board thinks Keough killed, meaning Perry and Keough perjured themselves earlier. Later that night Van Meter goes to Orchard and Sidwell's house and takes the money the two stole from the safe, indicating that the two work for him. That night Keough is shown having sex with a woman who is also a police officer (Michael Michele); the relationship is casual, and they do not reveal their surnames to one another.
The next morning Van Meter tells Perry and Keough to investigate the convenience store murder-robbery. Their investigation ends with them finding Orchard and Sidwell as lead suspects; when this is brought to Van Meter, he tells them to pin it on someone else and provides a false alibi for Orchard and Sidwell. Meanwhile, Assistant Chief Arthur Holland (Ving Rhames) finds Perry's actions suspicious and also does not believe Keough killed the man he was charged with killing at the Gun Board hearing. He asks his assistant Sergeant Beth Williamson, who has a mutual fling with Keough, to help him. When Williamson is pulling files on Perry and Keough, she discovers the identity of her lover to be Keough.
Later in the night, after obtaining a search warrant with underhanded techniques, a SWAT team raids the house of the ex-cons who are to be the fall guys. One of the ex-cons escapes and goes into a back alley, but is chased by Perry and Keough. When they catch up, Perry tells Keough to kill the man, but Keough has trouble pulling the trigger. Ultimately, however, Keough does kill the innocent man and is visibly shaken. Later on, Perry arrives at home mid-day and sees a moving truck outside of his house. His wife informs him that she is leaving him for another man. Perry tells her that she can keep the house, and leaves. Keough, still distraught after shooting an unarmed man begging for his life, goes to Williamson's house and confesses to her that he killed the man under Perry's orders. During this time, Van Meter decides he wants Perry killed and calls Orchard and Sidwell to do the job.
Van Meter calls Perry and tells him that there is a witness at the address 12657 Juliet. Perry initially balks at this proposal, citing the fact that this "witness" was not directly involved, and that this suggested murder would be far different. He finally accepts, and the call ends. Perry then runs the address 12657 Juliet with the department, and it is uncovered to be the address of Orchard and Sidwell. Shocked at this revelation, Perry ultimately decides to arm himself and head out to the address anyways, perhaps to kill Orchard and Sidwell. This links back to the start of the film.
Believing that Perry was sent by Van Meter to Orchard and Sidwell (as they are unaware of Van Meter's ambush for Perry), Keough and Williamson also drive to 12657