Det. Rose 'Phil' Phillips, member of a homicide squad in Portland, Oregon, is appointed as the Women's Coordinator, sparking jealousy in her male colleagues. However, her partner and friend Det. Frank Fusco disappears, frightening his wife and daughter. IA soon gets involved, led by tough investigator Det. James Vitelli.
After the death of LeBlanc and Fusco and the arrest of a third police officer, the homicide division is understaffed. Meanwhile, Phil investigates the case of a possible serial killer who inscribes a strange symbol at his crime scenes.
Shane Fusco's friend is kidnapped from the park, where she and Shane were out for a walk. Phil gets involved, investigating the kidnapping and questioning Shane about what had happened, and is helped by Detective Beck, a new member of the squad -- who is an expert in such cases.
Rita is found murdered. As a result, Shane's personality changes, and she becomes distant and withdrawn from the world as well as from Phil. Papadakis, another new detective, helps Phil and Beck investigate the murder.
Phil and Beck are at a restaurant when they observe a husband abusing his wife. Angered, Phil threatens to arrest the man. The wife later ends up dead, and Phil is determined to nail the husband for the crime.
Phil goes after a man whom she thinks killed his wife. Meanwhile, Phil's affair with Vitelli is leaked to the press. Martin Fox, a famous attorney hired to defend the husband, alleges a police cover-up. The adverse publicity prompts a visit by Phil's estranged father.
A body is found in the debris of a burned warehouse, and Phil and the other detectives investigate. They suspect street kids who live nearby, particularly Johnny, who may be responsible for previous arsons. Meanwhile, Vitelli investigates a leak from the precinct to the press. Also, Lieutenant Schwarz's daughter has surprising news.
A businessman is found shot to death in bed. The evidence seems to implicate his daughter, who claims he molested her. Complicating the investigation, however, is the fact that she has no memory of the night he was killed.
Phil is involved when a female cop charges a city official with sexual harassment. Tension develops between Vitelli and Phil, however, when Internal Affairs takes over the case. Meanwhile, Doc gains an admirer when Shane Fusco visits the station.
A Korean spa owner is murdered; but when Phil and Beck investigate, racial tensions make the case a touchy one -- especially when they learn the man had been buying up property in a predominantly black neighborhood.
Convicted of manslaughter and having served his time, an ex-con priest seeks redemption by running a halfway house. His efforts are stopped short, however, when he becomes a suspect in the murder of a newspaper reporter.
Lt. Schwartz takes the lead on a new case that unpleasantly resembles one he handled 25 years earlier -- one in which the suspect was released on a technicality -- hoping for a better result this time.
While Lt. Schwartz is absent, Phil is busy running the station. The squad investigates a gangland-style hit on a police officer; but as the case progresses, there is interference from the FBI. Meanwhile, Vitelli sees his father.
When Det. Clarke fatally shoots a murder suspect's brother, the real suspect threatens retribution. During the resulting investigation, tempers flare as Internal Affairs questions the detectives. Meanwhile, Lt. Schwarz announces his engagement. This means Farnsworth's return, which triggers Vitelli's jealousy. A gunfight follows at the wedding, where Doc shoots the murder suspect. The series ends as Phil is apparently fatally wounded.