Mannion goes west to take some rest from Ella's death and his recent dismissal. During a game of golf in Arizona, he finds a severed human finger on the course and brings it to a local sheriff, beginning an investigation that leads them to a Mexican drug lord and dirty cops. Meanwhile, back in D.C., Mannion's ex-wife Sherry meets Vanessa when she arrives at headquarters looking for him.

Mannion copes with Ella's death from a stroke, but it could bring hope to a boy waiting for a heart transplant. In the meantime, Mannion helps Clive look for Ricky and Temple and Debreno search for the man who shot one of their informants.

A moving tribute to Lynne Thigpen who died shortly before this episode. 

The mayor blames Mannion for riots in the streets when the chief refuses to fire an officer accused of police brutality. In other events, a friend and informant of Temple's is injured during a drug deal and Ella's husband gives Mannion some alarming news.

The mayor is more determined to have Mannion fired when a man is arrested and allegedly dies in custody because of an officer's failure to follow procedures. Things get even more intense when the mayor's mentally disturbed son disappears after two cops take him to a hospital.

Mannion trails a killer targeting interracial couples, one of whom is a black councilman married to a white woman. Back at the office, Ella finds evidence that implies an officer up for a commendation could be an arsonist. In the meantime, Nancy arrests her father for soliciting a prostitute and Temple helps a junkie kick his drug habit.
 

Mannion takes on a powerful city commissioner he believes is partially to blame for the cutbacks that have forced the chief to lay off officers. The move makes the mayor so upset he looks for an excuse to fire Mannion. Meanwhile, a congressional witness in a fraud trial claims that important documents were stolen from his hotel room and Nancy and Brander get hurt in an accident while pursuing a suspect.

Mannion's old partner arrives from New York and gets involved in a murder investigation. In the meantime, a woman scheduled to testify in a fatal shooting case in Chicago talks Debreno and Nancy into letting her visit her daughter first and Ella believes that an officer being hailed as a hero for rescuing a woman from a building burning isn't telling the whole truth.

Debreno is assigned to protect a popular singer set to perform at the Kennedy Center Honors who's received a death threat. In other events, Mannion becomes a uniformed cop in order to lead by example and Clive argues with Ella over her turning down a job in the mayor's office without having a discussion first.

While in L.A., Mannion unexpectedly meets up with Vanessa Cavanaugh and offers her a ride. Unfortunately, the pair find themselves stranded in a deserted part of town after their rental gets carjacked. Back in Washington, Deputy Mayor Lockhart asks Debreno to help her find a blackmailer who has a scandalous videotape that could destroy her career; Kendall is threatened by her ex-boyfriend; and the mayor offers Ella a job.

Police headquarters is quarantined when a man in custody appears to have an unknown infectious virus.

A law student attempts to commit the perfect crime by killing a stranger, confessing to the murder and recanting the confession. Meanwhile, Nancy tries to figure out the identity of a dead girl found in an alley and Kendall tries to end her relationship with a married man.

Mannion comforts a friend dying of AIDS. In other events, $500,000 worth of cocaine disappears from the evidence warehouse, Ella is sued by a man after saving him from a near fatal fall and Temple isn't sure what to do when a woman in the gun lab comes onto him.

On Christmas, Temple and Debreno look for three men disguised as elves who stole a mission full of donations to help feed 2,000 homeless people, Mannion dresses as Santa and promises an eight year old boy that he'll bring his mother home from prison and Nancy and Brander find a baby in a manger scene.

A boxing champion's wife is found murdered in her hotel room and Temple comes under suspicion due to a past relationship with the victim, who had been abused by her husband. In the meantime, a custodial worker is discovered to have a fake identity.

A reporter accuses Mannion of committing a war crime in Vietnam 32 years ago by ordering 18 innocent civilians to be killed, and one of the chief's fellow soldiers confirms the story. Also, Temple and Debreno search for a  fifteen year old boy they suspect is planning a murder for his gang initiation.

Noland shoots a college student he thought was going to rob a convenience store, but the investigation fails to turn up a weapon. To make things worse, Internal Affairs demands that Noland be suspended and the student's wealthy parents threaten to press charges.

Mannion gets another chance to capture a contract killer who eluded him 25 years ago when the chief learns the hitman is in D.C. In other events, Nancy gets hurt while pursuing a purse snatcher and receives more bad news in the hospital, Kendall has to apologize for allowing her picture to be taken with a mayoral candidate who's critical of the police department and Ella begins to question whether she should get married.

Debreno's priest brother is shot by a sniper while performing a funeral service and the investigation leads to a lawsuit against another priest charged with sexual misconduct. Meanwhile, Nancy becomes obsessed with learning the identity of a young woman whose body she discovered.

Mannion investigates a series of robberies where pharmaceuticals, most of them for AIDS, are stolen. In other events, Temple worries about taking a random drug test since he failed to report using cocaine while undercover and Debreno is won by a mayoral candidate in a charity bachelor auction.

Mannion fights for legislation against child pornography when an eleven year old girl whose picture was on a porn site is found dead. He also butts heads with a civil rights attorney on a case where a cop is charged with using excessive force.

Still presumed dead, Mannion heads to Paris to follow the Government official he suspects is responsible for the attempt on his life. Meanwhile, back in D.C., Temple is pulled over for speeding and an officer finds cocaine in his car, but Temple swears the drugs are evidence he collected at a crime scene and forgot to turn in.

An aggressive U.S. attorney general pressures Noland to solve Mannion's disappearance after the chief is shot on his boat and falls overboard into the Potomac River. Little does everyone realize is that Mannion is in hiding to find out who's behind the shooting.