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.

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.

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.

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.

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.

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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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Mannion is determined to have the best people possible working for him and asks his ex-wife, Sherry, to become his Superintendent of Detectives. Meanwhile, when an ex-con is arrested for the murder of his girlfriend who was also a parolee, Mannion tries to put into action a parolee-rehabilitation program Ella had begun before she died.

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Mannion and the team reopen a 17-year-old cold case when a girl is found murdered in the streets of D.C. ""Jupiter,"" a serial killer that was never caught, appears to have re-emerged.