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.

Temple leads an investigation to catch a serial killer who is murdering prostitutes, but after viewing the women's mutilated bodies he doesn't know if he's strong enough to see the job through; Mannion comes under pressure to hire a politically correct candidate for a district-commander post.

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.

Chief Mannion and his men investigate the disappearance of teenage girls who all point to a virtual suspect: a guy named Icarus who uses the internet to lure his victims and eventually murders them. The case takes a personal turn when Noland's niece becomes the next target and Joe puts all his efforts into catching the guy. Meanwhile, Temple suffers with pranks and rash commentaries from his co-workers about the death of Lester Richards, while Sherry tries to adjust to her new job.

After Chief Strickland causes the death of an innocent old lady due to having inaccurate information on the whereabouts of a dangerous drug lord, Mannion decides to catch the guy himself. He uses the help of his best men, who put their jobs at steak and work parallel to Strickland's orders. Mannion's house is burnt down after he keeps stopping kids from selling drugs. When Mannion finally catches the guy, Mayor Douglas won't give his job back, so Jack is forced to reveal that he knows the phone wire was illegal, which ultimately forces Douglas to give him his job back. Meanwhile, Temple investigates two cops whom he thinks are abusing their authority and beating the people they arrest, while Debreno sleeps with Maria Rodriguez, which causes some conflict on his friendship with Temple.

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Mannion goes to New York to attend his ex-wife's wedding — and perhaps stop it; an ex-cop accuses Noland of covering up a case 30 years ago that involved a politician's son.

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.

Back from his Arizona vacation and determined to get his job back, Jack starts campaigning for being Chief of police, even though it's not an elected position. He chooses not to use the illegal taping card that might get him back in the office in no time for a future use and moves into a poor neighborhood. Meanwhile, Brander decides to go back to the force and teams up with Nancy to investigate Lester Richard's death, for which Temple got arrested. They discover that Maria ""Cashmere Brown"" Rodriguez was lying, which frees Temple – but doesn't exactly prove he didn't kill Lester vindictively.

Mannion wants to believe that it was self-defense when his attractive fencing teacher's husband is killed at her studio. Meanwhile, Debreno recognizes a suspect in a drug case as his childhood friend who convinced Debreno to go into the Police Academy.

The threat of biological terrorism strikes Washington and Chief Mannion has to arrange almost all his force to search for a potential terrorist. An escapee from juvenile detention murders a taxi driver and a few drug dealers and becomes a big threat once he hides in a public schools, putting in danger hundreds of lives. Temple disguises as a student to catch the killer, in an operation that almost cost Ella the guard of her nephew, if it wasn't for Mannion's interference to the judge.

A respected Vietnamese colonel, who is now a successful local businessman, is suspected of running a sex-slave operation using kidnapped Asian girls, one of whom is murdered. Also, Ricky refuses to go to school and he won't tell Ella why; and McGregor's reluctance to publicly acknowledge his relationship with Nancy leads to a confrontation.

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.

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.

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.

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.

Mannion is very disappointed when he finds that the 17-year old boy who got Ella's heart is involved in a robbery of a gas station that ended in the attendant's death. Temple's day turns very sour when the mayor decides to not pick up the court fees after the Lester Richards case. Meanwhile, Nancy and her mom are attacked by car jackers, or are they?

Mannion investigates the death of terminal patient afer her daughter shoots the doctor at point blank range, who she believes is responsible for her mother's death. Meanwhile Nancy must confront her own future when her father's Huntington's Disease worsens.

Mannion goes after a dealer who is supplying drugs to rich executives. Meanwhile, his ex-wife, Sherry, shows up unexpectedly to deliver bad news.

Mannion attempts to reunite a troubled boy living in foster care with his mother, who is in jail on a drug charge; McGregor tries to prevent a stalker from harming a woman; a female reporter shadows Mannion to write a profile of him; and Temple raises doubts about his upcoming wedding.

Mannion vows to better protect cab drivers after a cabbie fatally shoots a passenger he thought was trying to rob him. Also, a new U.S. Attorney stirs up controversy, and McGregor gets jealous when Nancy receives flowers from an unknown person.

Mannion receives Monya's hand by the mail, an indication that someone is plotting against him. Temple hasn't recovered from his fiancée's death, but Mannion accepts him back on the force. With Mannion under heavy investigation, the mayor has no options but suspend him. Noland steps in as police chief. Noland assigns McGregor and Temple to work directly for Mannion and he decides to run a investigation of his own. Temple, McGregor and Mannion go to a contruction to investigate the Russian mob, since a scheme for money laudry in the value of over 1 billion is discovered. The FBI tapes two unidentified Russians talking about Mannion's murder, and the voices are identified to be Boris' (Mannion's informer) and Putin's (the man the FBI is after). McGregor and Temple see four suspects enter Boris's bar and call Mannion. Temple decides to take action and walks into the bar, despite Jack's order to wait for him. Temple starts a fight with the men, resulting in him being taken hostage by one of