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 goes head-to-head with the U.S. Attorney General and a tough civil-rights lawyer (Jaclyn Smith) in an emotionally charged episode. The investigation into the murder of an 11-year-old girl turns up the child's photo on a porn site, prompting Mannion to seek help from Attorney General Hatcher to toughen legislation against Internet child pornography. But Hatcher has an agenda of his own. In other cases, the chief is asked by a congressman to look into a case involving the alleged accidental death of his son, and a high-profile lawyer (Smith) accuses an officer of using excessive force.

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.

After a man crashes and dies and the police finds thousands of dollars with him, Mannion and his men start an investigation to prevent the dead guy's old girlfriend from being killed. Turns out an old shooter that killed one of Mannion's friend back in New York years ago is the hired killer they're looking for, and the woman they were protecting was behind the plan to kill her current husband and keep the money. It's Jack's second and final chance to catch the guy. Mannion hires a personal wedding dress designer for Ella, who has second thoughts about her marriage. Nancy is diagnosed with Huntington's disease after falling from a fire escape and suffering a concussion while chasing a criminal.

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.

The wife of a heavyweight boxing champion is found murdered in her hotel room, and Temple, the first officer on the scene, comes under suspicion because of a past relationship with the victim, who was habitually abused by her husband. Also: a custodial worker at the police department is discovered to have a false identity.

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.

Mannion tells Jenny McLure how his men arrested her brother while she is waiting for her final day. Jenny is dying from AIDS and Mannion makes sure her last days are filled with company and happiness. The cocaine found at Lester's apartment is missing, and Parras becomes of the main targets on the investigation on who switched the coke with sugar. Without the evidence they can't put Lester away, while matches from his pistol are coming from numerous murder scenes. Finally Chief Mannion finds the mole and sends Lester to jail, but unfortunately Jenny doesn't last to see the next morning: she passes away the day before Mannion's event to raise people's awareness on the danger and prevention of AIDS.

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.

Debreno is assigned to protect a country singer, scheduled to sing at the Kennedy Center Honors, who's receiving death threats; Elsewhere, in an effort to lead by example, Mannion hits the streets as a uniformed cop to make quality-of-life arrests on charges such as disorderly conduct, gambling and prostitution. But one of his arrests sparks a chain of events that leads to the reopening of a cold-case murder.

Mannion's uncle, a retired New York City cop, visits and immediately gets involved in a murder case/jewelry heist; Debreno and Nancy transport a woman who witnessed a fatal shooting to Chicago, where she is scheduled to testify. But, she persuades her escorts to let her first visit her estranged daughter.

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.

After a black prostitute is found murdered with the inscription ""Respect the Order"" attached to her body, Mannion and his team start a deep investigation that leads to a racial criminal who started serial killing African-Americans who were involved with white people. Meanwhile, Parras sees her father being arrested for requesting the services of a prostitute and has to face her own family problems. Temple helps a friend detox from heroine and Ella investigates a suspicious fire that could promote an officer – but ends up being the reason for his arrest.

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.

After a video where Brander arrests a drug addict is made public and turned into a abuse of power issue, the Mayor demands that Mannion fires Brander, which he refuses to do giving that the man was found innocent. Instantly, a major riot breaks out in the city, with the citizens protesting and attacking the police, demanding that Brander gets fired. Several police cars are bombed and set on fire, and Nancy rescues an officer from an angry riot. He's badly injured, and asks her out when he comes by to pick up his dog. Meanwhile, Temple witnesses his friend Reese die while trying to find the man who shot him. Mannion is trying to save Brander, but when he can no longer live with his guilt he turns in his badge. Unfortunately, the mayor taped Mannion's conversation with Brander over the phone and fired him for obstruction of justice. Late at night, Clive calls him up, saying that Ella died unexpectedly.

After beloved Ella Farmer dies unexpectedly, all the members of the police district pay a tribute to her, remembering all the hard work and effort she put in her job. They pray together and miss her, knowing she'll be forever in their heart, and that no one can ever replace her as Mannion's right arm.

Without a job and his best friend, Jack takes off to Arizona to play some golf, but not even without his badge he can stop solving crimes. He gets himself involved in a scheme of dirty cops with Mexican dealers and crosses the border to catch the dealer – which he does. Meanwhile, back in D.C., Cavanaugh and Sherry team up to trace Jack and Cavanaugh discovers something that might save Jack's job. Nancy does some investigation on her own and discovers that the guy that died on Brander's hand was injured prior to their encounter, which could clear Brander. Temple and Debreno set up a scheme with Cashmere Brown to bust Lester Richards, who ends up shot to death by Temple.

When Mannion has Temple and Debreno investigate the woman's murder, he discovers that the criminals weren't going for the victim's cash or credit cards, but for the expensive purse itself. In response, Mannion immediately dispatches detectives to patrol subway cars, angering the chief of the Transit Authority, who believes that Mannion is trying to muscle in on his territory. Then, when Debreno and Temple set up a sting operation, Debreno's life is put in danger and Mannion's team must find a way to draw out the perpetrators of these crimes before they strike again. Also, Mannion's outrageous ex-fiancee comes back for a visit after hearing that Mannion and Sherry split up.

Mannion issues a mandate to get illegal guns off the streets and uncovers the surprising motive behind the murder of a well-connected young man.

People in the witness protection program become victims, and the team sets out on the case to find the killer. Meanwhile, Chief Mannion gets a specialty sandwich named after him, which then becomes ""hard to swallow.""