Season 1 (2002)

Captain David Aceveda, seeking to usurp the current black City Council representative of Farmington by swaying the Latino vote, looks to rid his precinct, The Barn, of corruption, starting with Detective Vic Mackey and the controversial yet effective Strike Team that Mackey leads. Aceveda works with the Justice Department to bring Detective Terry Crowley onto the Strike Team to try to gain evidence to use on Vic. However, Vic is aware of Terry's informing due to his friendship with the Assistant Chief of Police, Ben Gilroy.

When the Strike Team conducts a raid on the residence of Two-Time, a drug dealer, Vic and Strike Team member Detective Shane Vendrell are shot at by Two-Time, who they fire back at and kill. Vic picks up Two-Time's gun off his body and shoots Terry in the face (without informing follow Team members Detective Curtis "Lem" Lemansky and Detective Ronnie Gardocki), making it look like Terry was murdered by Two-Time himself. Gilroy assists Vic in covering up the murder, which stops Aceveda's investigation. Things come to a breaking point towards the end of the season when Gilroy's own ambitions threaten both Vic's and Aceveda's futures.

Separately, rookie officer Julien Lowe learns the ropes from his training officer Danielle "Danny" Sofer, while attempting to hide his homosexuality from other officers. Julien witnesses the Strike Team smuggling a portion of a drug bust for their own personal wealth and reports it to Aceveda. When Aceveda begins to investigate Julien's claims, Vic threatens to reveal Julien's homosexuality to the department, causing Julien to back out from his witness statement and leaving Aceveda with nothing to go on.

Partners Detective Holland "Dutch" Wagenbach and Detective Claudette Wyms hunt a serial killer targeting prostitutes while dealing with their own problems in The Barn. Vic, separately, has to deal with the growing rift between him and his wife Corrine. After learning his son Matthew is autistic, Vic uses his illicit police activities to pay for special schooling for him. Due to Vic's reckless behavior, Corrine takes the children and disappears, leaving a note to Vic to not to come find them.

Season 2 (2003)

The Barn discovers that the Mexican drug gangs in Farmington are uniting under a new drug lord, Armadillo Quintero, who is able to evade arrest due to lack of evidence and willing witnesses. Privately, the Strike Team learns that Armadillo has knowledge of some of their illicit activities and fear he will rat them out if he is taken to prison. They attempt to coerce Armadillo to return to Mexico by threatening to "greenlight" Armadillo's brother Navaro. Armadillo responds by having Navaro murdered himself. After Armadillo murders one of Vic's CI's, Vic loses his cool and burns half of Armadillo's face on a stove burner only for Armadillo to later retaliate by doing the same to Ronnie and using his new leverage against the Strike Team.

With the fallout of Gilroy's arrest, Vic and Aceveda find themselves under scrutiny of an independent auditor who is determined to find and expose any corruption in The Barn. As Vic and Aceveda struggle to stay one step ahead, their tactics draw the ire of Claudette, who is determined to arrest Armadillo after he rapes a young girl. Claudette, initially reluctant to take a leadership role, eventually agrees to take over as The Barn's Captain after realizing she can't stay neutral anymore. Meanwhile, Danny fatally shoots a Muslim man who threatened her during a confrontation and Julien is unable to corroborate her story. The man's widow threatens to sue the department and creates problems for Danny both professionally and personally.

Shane and Lem convince a small-time criminal to kill Armadillo by passing him a knife after he is arrested and put into the cage by Danny, leading to Danny being fired. Separately, Vic hires a private investigator to search for Corrine and the children, and discovers her seemingly preparing to file for divorce. He moves out of his home and preemptively files first in an attempt to gain a better chance of retaining his parenting rights, but this only serves to widen the distance between him and Corrine.

As the Armadillo case is resolved, the Strike Team learn that the Armenian Mob have a "money train" that passes through Farmington every so often, a means for the mob to launder their illegal funds into untraceable cash. The Strike Team privately plans to rob the money train, knowing that they would be financially secure for a long time should they succeed. The money train heist is successful, while Aceveda wins the city council primary.^[5]

Season 3 (2004)

In the aftermath of the money train heist, the Strike Team resolves to lie low and avoid any controversy but quickly find themselves marginalized and lacking vital information. When some of the money from the heist is revealed to be marked for a federal case, the Team struggles to stay ahead of Dutch, who begins to suspect Vic. The Armenian mob sends hitman Margos Dezerian to find the money and kill anyone suspected of involvement in the robbery. As both Margos and the investigation close in on the Strike Team, a fearful Lem burns a majority of the money in a desperate attempt to protect the Team, ultimately leading to a confrontation which causes the group to disband.

Claudette is promised a promotion to Captain and maintains a supervising role while Aceveda prepares to move on to the city council. However, a defense attorney is killed, and the ensuing investigation leads Claudette and Dutch to discover that the victim had been a heavy drug user for the past three years. Claudette, determined to ensure justice, investigates further, losing favor with the D.A. and Barn coworkers after she reopens the attorney's closed cases against orders and resulting in her being denied the promotion to Captain.

Shane enters a serious relationship with a woman named Mara and eventually proposes to her when she reveals her pregnancy. Mara encourages Shane to be more independent from Vic, even after discovering the money from the heist. This conflict between Vic and Shane soon becomes personal, leaving a deep rift between the two.

Dutch opens a case of a serial rapist and finds himself becoming more obsessed than usual without Claudette's backing. Julien, having suffering a beating from his coworkers after being outed as gay, has toughened considerably, leading Claudette to feel alarmed that he may wash out. Danny makes a deal with Aceveda to be reinstated provided she give him pertinent information about other officers.^[6]

Season 4 (2005)

Monica Rawling (Glenn Close) takes over the role as Farmington's new captain, and implements federal asset forfeiture laws to seize any property tied to drug dealing, using the money to fund the department and give back to the community. This soon becomes controversial among The Barn, particularly Julien, and members of the Farmington community. After the Strike Team's disbandment, Shane works in Vice with new partner Armando "Army" Renta (Michael Peña). The pair enter into a dangerous situation when trying to control major drug lord Antwon Mitchell (Anthony Anderson), who blackmails them and coerces Shane into accepting an order to kill Vic. The police are outraged after two officers are kidnapped and subsequently found murdered. In the end, the Strike Team is re-formed and manages to put Antwon in prison. Rawling eventually loses her position over a dispute with the DEA.

Meanwhile, Dutch and Claudette are "blacklisted" as detectives because of the latter's refusal to apologize to the D.A. after her reopening the cases of the murdered defense attorney resulted in many of the prosecutor's cases being overturned. Dutch attempts to resolve the situation by making a back-room deal with the D.A. to keep an eye on Claudette and do favors for the office in return for breaking back into action. Ultimately, this causes a rift between the partners, culminating in a confrontation where Claudette rebukes Dutch for making the deal.^[7][8]

Season 5 (2006)

Internal Affairs Division Lieutenant Jon Kavanaugh (Forest Whitaker) begins an investigation into Vic and the Strike Team. Previously, Lem had stolen heroin as leverage for information on the disappearance of a young girl he was close to. Emolia Melendez, an informant, witnessed the theft and reported it to IAD. Finding the heroin gave IAD sufficient evidence to arrest Lem, but Kavanaugh, suspecting that Vic murdered Terry Crowley, informs Lem of his theory and coerces Lem into wearing a wire to get evidence on the Strike Team. Lem is able to warn Vic that he is wired and Mackey uses it against Kavanaugh to embarrass him and IAD.

Kavanaugh responds by moving his investigation into the Barn, causing anxiety for everyone inside. Applying pressure to the team in any way he can, Kavanaugh finds out about Mackey's share of the money train haul after interrogating Corrine. Kavanaugh's mentally ill wife Sadie comes into play when she falsely accuses a man of raping her. Vic and Lem view a personal conversation between Kavanaugh and Sadie from the interrogation room camera, which Kavanaugh quickly realizes is turned on. He rushes out in a rage, and Vic and Lem quickly exit the security monitor room, but Kavanaugh sees them and arrests Lem on the spot.

Kavanaugh freezes the Strike Team's assets but Vic manages to secure bail money for Lem and assists in providing safe passage for him to leave the country. However, Shane worries Lem will turn. Kavanaugh orders Aceveda to lie to Vic and say that Lem had revealed the Strike Team's involvement in the robbery of the Armenian money train. Shane falls for the deception and murders Lem with a hand grenade. After Lem's body is discovered, Vic vows to find the killer.

Other plots include Dutch discovering Claudette has lupus and Claudette's subsequently reaching her physical breaking point after finally getting a serial killer from their past to confess. Steve Billings functions as the interim "jellyfish yes-man" Captain of the Barn while Danny deals with pregnancy and refuses to divulge the baby's father, who is eventually revealed to be Vic. Julien trains Tina, a beautiful but incompetent rookie officer, and at long last Claudette gets her opportunity for promotion to captain of the Barn, which she accepts on the sole condition that she gets to run the Barn her way.^[12][13]

Season 6 (2007)

Vic and the Strike Team are distraught over Lem's death. Shane, overcome by guilt, becomes reckless and suicidal and enters into an affair with a teenager associated with the new One-Niner boss. Kavanaugh, convinced that Vic killed Lem and desperate to close his case after being given a 24-hour turnaround deadline by the Assistant Chief, resorts to planting evidence and coercing witnesses to lie about the Strike Team. Dutch and Claudette begin to suspect Kavanaugh's integrity after holes in his investigation are discovered and Corrine reveals that Kavanaugh sexually assaulted her. Kavanaugh eventually confesses to his actions and is arrested.

Vic and Ronnie hunt Guardo Lima, a drug lord and overseer of a grenade factory that the Barn raided prior to Lem's death, where Shane pocketed the grenade he later used to kill Lem. After capturing Guardo, Vic tortures and murders him while Shane and Ronnie watch. Shane's subsequent behavior arouses suspicion in Vic and Ronnie, and after reviewing a report by Kavanaugh of the night Lem was killed, they both realize the truth. Vic gets Shane to confess, but Shane threatens to reveal the Strike Team's illegal exploits should Vic attempt to arrest him. Shane tries to get protection with the Armenians and recklessly reveals Vic was the ringleader behind the money train robbery, putting Vic's family in danger. However, Shane takes steps to rectify this mistake, kidnapping Corrine and Vic's daughter Cassidy before ambushing and severely wounding the Armenian hitman sent to kill them.

Vic learns from Claudette that the Chief plans to force him into early retirement. Claudette makes strong efforts to solve a brutal mass murder after learning the Barn could be shut down if no improvements are made by the time quarterly crime statistics are released. Julien joins the Strike Team under the leadership of Kevin Hiatt, brought in as Vic's replacement but nowhere near as effective as Vic. Aceveda finds a new backer for his mayoral campaign, real estate developer Cruz Pezuela. After Pezuela begins offering information into the pending San Marcos massacre investigation, Vic discovers that Pezuela has ties to the Mexican cartel and attempts to use this as blackmail against Pezuela to save his own job. In turn, Pezuela offers him a photo of Aceveda's sexual assault. Vic initially tries to use the photo against Aceveda, but the two eventually ally to take down Pezuela. Vic confronts Mexican intel operative Luis Aramboles and, upon searching the trunk of Aramboles' car, discovers a box filled with blackmail on government officials in Farmington. Vic and Aceveda plot to use this to serve their own respective interests.

Season 7 (2008)

Vic spins the blackmail box into a gang war between the Mexicans and Armenians as a way to protect himself and his family after Shane's reveal to the Armenians that Vic spearheaded the money train robbery. As the gang war spins out of control, Vic cozies up to ICE Agent Olivia Murray as a way to bring more weight down on the cartel and to secure an ICE position for himself and Ronnie, along with complete immunity for their past crimes.

Shane, despite holding his written confession as leverage over Vic and Ronnie, agrees to help stop the Armenian threat in order to protect his own family. Vic and Ronnie inform Shane of a plan to set up an arranged meeting between the Mexicans and Armenians with Shane as the middleman. Unbeknownst to Shane, Vic and Ronnie formulated the plan as a way to resolve all of their issues, including vengeance for Lem. Ronnie tampers with his sidearm in an attempt to get him killed by Mexican hitmen sent to kill Rezian and his men, who, along with Shane, think the meeting is to purchase the blackmail box that would subsequently be given back to Pezuela and end the gang war. Shane escapes and, after realizing that his partners set him up to die, blackmails a pimp from a previous investigation to help him perform simultaneous hits on Vic and Ronnie. The attempt fails and the pimp gives up Shane, forcing Shane to go on the run with Mara and their son Jackson.

Vic turns in his badge in order to focus on catching and killing Shane and the pregnant Mara. Mara uses Shane's leverage against Vic to coerce Corrine into serving as a middleman to help their family escape the police. Vic fails an attempt on Shane and Mara's lives after tracking them down to a hospital using information from both Corrine and Ronnie, driving Corrine to her breaking point. She contacts the Barn and agrees to help stop Vic as long as he never learns of her involvement. Dutch and Claudette begin a full-scale investigation into Vic and Ronnie in a final attempt to take down the remaining Strike Team members once and for all. After a failed attempt to incriminate Vic in the act of aiding and abetting Shane, Dutch fakes the arrest of Corrine in order to preserve her cover.

Vic, believing that Corrine was actually arrested, leverages the bust of the Mexican cartel into a full immunity for both of them. As part of his deal with ICE, Vic confesses to all the crimes he and Strike Team committed, incriminating Ronnie in the process and stunning Olivia and her boss, as well as Claudette and Dutch, who walk in too late to stop the deal. Claudette, her health still deteriorating, nearly breaks down upon learning of Vic's immunity. As a small bit of revenge and to protect Corrine, Claudette and Dutch make an arrangement with Olivia to place Corrine, Cassidy, Matthew, and Megan into federal witness protection.

Meanwhile, Shane, Mara, and Jackson return home after Mara is injured during a robbery. Shane attempts to blackmail Vic one final time, but Vic gloats to Shane about his immunity deal and Shane's inability to use the Strike Team's crimes as leverage. Shane, trying to prove he was always the better husband and father, reveals Corrine's betrayal. Officially out of options, Shane goes back to the house, where a neighbor spots him. He poisons Mara and Jackson and shoots himself after writing out his confession as Claudette and her team arrive to arrest him.

Vic and Ronnie lead the cartel and the leadership of the black gangs into an ICE trap, which Aceveda uses as a publicity stunt for his mayoral campaign. They return to the Barn, where Vic is informed by Claudette of Shane’s suicide. She orders him to the interrogation room and reads Shane's suicide note before placing the crime scene photos of Shane, Mara, and Jackson's corpses on the table and leaving the room. Realizing that Claudette is watching his reaction in the security monitor room, Vic stares into the camera before ripping it out of the wall in a rage. As Vic exits the room, he furiously says to bill him for it and Claudette replies that the "first payment's due now", before prompting Dutch to arrest Ronnie publicly for all the crimes Vic confessed to. Ronnie, led to believe that Vic that he had gotten immunity for both of them, screams that Vic betrayed him as Vic attempts to explain his actions. Ronnie is dragged from the premises as the entire Barn stares at Vic in contempt.

Later, Claudette admits to Dutch she’s dying but will remain Captain as long as she can while Corrine and the children arrive at their new home. Olivia, angry that Vic used her, relegates him to a job writing daily analysis reports at a desk for ICE. Vic, shocked by this information after assuming he'd be working on the street, argues it wasn’t the terms he agreed to, but Olivia reminds him that any step out of line to the word of their agreement will violate the terms of his immunity. In the final scene, Vic sits at his desk in the ICE office after hours, where he unpacks pictures of his children, as well as one of himself and Lem. After hearing police sirens, he rushes to the window and stares out at the street below before returning to his desk, removing his gun from a lockbox, and leaving.