The third-season opener picks up where the sophomore year ended, with Mannion struggling for his life after being shot on his boat and falling overboard into the Potomac River. As he tries to pull himself ashore, his would-be assassin — the daughter of a Russian mobster — flees the scene and is hit by a car. While the accident brings to light the fact that Mannion is missing, the chief keeps his survival a secret so he can figure out who's behind the shooting. Deputy chief Noland is immediately pressured to solve the case by an aggressive U.S. attorney general, while a new press secretary tries to keep matters from spinning out of control.

Mannion, who is presumed to be dead, pops up in Paris to follow the Government official he believes is behind the attempt on his life. Back in Washington, D.C., Temple is stopped for speeding and an officer finds cocaine in the car, but Temple claims the drugs are evidence he obtained at a crime scene and forgot to turn in.

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).

On Christmas Eve, Temple and Debreno hunt for three dwarfs disguised as elves who robbed a mission truck and were responsible for other thefts in the area, a billy goat who was part of a real-life nativity scene goes missing, Mannion is determined to fulfill ""Santa's"" promise to an 8 year old boy; Parras becomes attached to an abandoned newborn, and Ella has a gift-giving mix-up.

One of Vanessa Cavanaugh's students commits what she taught to be a perfect murder. No evidence, no witnesses. After the murder confesses to Temple and Debreno his crime, he starts to play with Mannion, who can't seem to charge him since the confession wasn't recorded. Mannion is out to get him for the murder of the father of 3 children and ends up finding a way to link the suspect to the murder scene. Meanwhile, Parras works on a Jane Doe case and finds the victim's estranged mother; and Kendall finds it difficult to end her relationship with a married man.

A doctor who was reporting a crime sees Brander bring in a foreign criminal with a very suspicious disease, which she thinks might be Ebola. Instantly the office is put in quarantine. Without being able to get out, Mannion has to count on Ella, who was at home preparing for her wedding to keep the order while he breaks through Brander's isolation bubble to save his life. Meanwhile, Debreno drives in the snow to find a delirious Temple, who was exposed to the bacteria and might be contaminated with what was later discovered to be a harmless African flu. The next day they all attend Ella's wedding, where Ricky calls her 'mom' for the first time.

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.

The mayor is more determined to remove Mannion from office after a man is arrested and dies while in custody, apparently, due to an officer's failure to follow proper procedures. Things get even more intense between the two rivals when the mayor's mentally disturbed son goes missing after being taken to a hospital by two cops.