Mannion investigates a series of robberies in which pharmaceuticals, mostly AIDS medications, were stolen; Temple worries about having to take a random drug test because of his failure to report that he used cocaine while undercover; Debreno reluctantly agrees to participate in a charity bachelor auction and is won by a sexy mayoral candidate (Kelly Rutherford).

When father Patrick Debreno is shot at a funeral, Mannion and his team start an investigation to discover who the shooter is. They search through Monsignor Banning (father Debreno's mentor) past and discover accusations against him on sexual abuse against a child. Suspecting that father Debreno was not the target, Mannion reopens the case and the mother of a molested child gives herself in. Meanwhile, Ella struggles to balance her time between work and Clive, while the characters reflect on their faith during the course of the episode.

During a struggle, deputy chief Noland shoots a college student he believes is about to rob a convenience store with a gun, but the ensuing investigation doesn't turn up a weapon. Soon, Internal Affairs demands that Noland be suspended, but Mannion refuses to take his badge. Also, the student's wealthy parents threaten to bring charges against Noland.

A reporter accuses Mannion of committing a war crime in Vietnam 22 years ago by ordering 18 innocent people to be killed, and one of the chief's fellow soldiers confirms the story. Also: Temple and Debreno search for a 15-year-old boy they suspect is planning to carry out a murder in order to join a gang.

While in L.A. Mannion unexpectedly meets up with Vanessa Cavanaugh and offers her a ride. Unfortunately the rental care is carjacked and the pair find themselves stranded in a deserted part of town after they get 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 Ella is offered a job by the mayor.

After a shrinking budget forces Mannion to lay off officers, he takes on a powerful city commissioner he believes is partly responsible for the cutbacks. But the move upsets the mayor, who then looks for an excuse to fire the chief. Also: a congressional witness in a fraud trial claims key case documents were stolen from his hotel room; and Nancy and Brander are injured in an accident while pursuing a suspect.