The Strike Team's new strategy is to play by the rules in order to keep the I.A.D. from sniffing around the money they stole from the Armenian money train. Unfortunately, their plan is abruptly interrupted when a routine drug bust lands them right in the middle of a high-powered gun running ring. Soon they find themselves racing to disarm two rival gangs before a race war breaks out. When an old ally turns out to be the new leader of the One-Niners, they use him to set up a sting gun buy. Tension among Vic and the Strike Team increases when Dutch and Claudette begin investigating the hug of two Armenian gangsters tied to the money train robbery. Meanwhile, with her promotion to Captain on the horizon, Claudette faces a cruel reality when David decides to not only stay in his position but also implement some of her ideas to help clean up Farmington. After his blanket party in Season Two, Julian's manhood and ability as a cop are in question and Vic urges him to take action to get some respect back from the barn. Danny makes a plea to Aceveda to get her job back and Shane deals with the pressures of keeping his new girlfriend happy without interfering with his job.
When Vic finds himself at odds with the Strike Team, he decides that the only way to bring down a gun running ring that is supplying rival gangs on the brink of war, is to use some cash from the Money Train. When the bust doesn't go down as expected and the Strike Team is overpowered by the Byz Lats, they find themselves out both the money and the guns. Just when Vic begins to plan drastic measures to bring down the Byz Lats and their supply of MP5's, Claudette and Dutch reveal a gang hug may be connected to the missing guns. The Strike Team works to settle the war between the two gangs, the Byz Lats and the One-Niners, by forcing the two leaders to draw battle lines. After Claudette and Dutch solve their gang murders, Vic is able to get the guns off the street. Claudette reveals to Vic that the undercover Decoy squad will be joining the Barn and she will be overseeing both them and the Strike Team. Julian's newfound confidence on the job raises some concerns around the Barn when a complaint is filed against him for excessive force. Danny returns to the barn when she gets her job back and finds that Julian isn't interested in being her partner anymore. Vic tries to correct the first impression he's made on Mara but she makes it clear she's only interested in Shane's wellbeing.
When Claudette takes control of both the Strike Team and the new Decoy Squad, their first assignment is a hooker sweep. What Vic thinks is a simple sweep, quickly becomes a nightmare when a prostitute, Farrah, is determined to bring down her pimp at any cost and wants Vic's help. When Claudette orders Vic to work with Farrah, he finds himself conflicted between Claudette's plan and Farrah's blackmail. Meanwhile Dutch discovers an elderly woman rape case with a sick twist is just the beginning of a disturbing pattern. David is forced to choose between his job as Captain and his future as Councilman when a man he knows and respects is arrested for solicitation during the sweep. Back on duty, Danny tries to get in good with Tommy and Julian by helping them on a stolen stereo bust and giving them the credit. After his run-in with Farrah, Vic decides to check up on Connie's son who is living in an overcrowded foster home. Meanwhile, tension rises between Shane and Mara when Shane feels the relationship is going too fast and Mara reveals she is pregnant.
When a high profile car jacking case involving a public official is declared by Aceveda as the Barn's main focus, the feuding Strike Team and Decoy Squad decide to place an unusual bet over who'll be the first to bust the culprit. The bet? Losing team has to streak the Barn. Dutch investigates an attempted hug case between two brothers that involves a repeated case of acute food poisoning. He uses hostile tactics to get a confession from one of the brothers whom he believes is at fault for trying to hug the other brother. With Claudette's absence due to overseeing the Decoy and Strike Team, Dutch soon finds himself in hot water and needs her help on the case to bail him out. As the two rival teams race to find the culprit of the car jacking case, tension between Shane and Tavon only gets worse and eventually explodes with shocking results when a fist fight leads to Tavon getting in a horrible car crash. Meanwhile Danny begins to think she'd be a better influence on Julien as a partner when she and Lucas respond to a domestic abuse call at Julien's house. Vic and the Strike Team eventually prevail and nab the car-jacking culprit, proving that they are still on top.
When Shane fails to show up at the hospital to see how Tavon is doing after his shocking car accident, Vic pays a visit to his apartment and immediately notices something amiss. Shane and Mara lie to cover up the fact that a unhappy fight between Shane and Tavon occurred. But Vic is on to Mara and Shane's involvement and soon gets the confession he expected. Vic keeps his cool and decides to take charge and help Shane and Mara further cover up what happened to protect the Strike Team. In the midst of the Tavon crisis, Claudette decides to appoint the Strike Team to a routine hooker sweep, despite Vic's protests. When Vic and his team flip a collar who's smuggling contraband into local prisons, they decide to abandon their routine hooker sweep to follow the lead on this bigger case. They're sidetracked when there's word that David has discovered a perp who may know something about the Money train heist and the men responsible. The strike team races to get David off the scent, but not before David gets himself in serious trouble with the darker side of Farmington. Meanwhile, Dutch discovers the Cuddler rapist has struck again. Danny and Julian take on a stalker case of a woman being harassed by her ex-boyfriend.
When Tommy's ex-wife and son are brutally cuddled and he is taken in for questioning by another district's detective, everyone at the Barn is outraged. With Julien and Danny's help, Vic takes matters into his own hands to prove Tommy's innocence. While Julien embraces Vic's strong-arm tactics, Danny isn't as comfortable going against the book. Honoring her agreement she made with Aceveda that got her job back, she informs David that Julien and the Strike Team have posse'd up to track down the hugger. But during their hunt, Vic and Julien discover an ugly truth that puts Tommy's innocence into question. Meanwhile, David decides to hold a press conference regarding the Cuddler rapist and passes the baton to Dutch. But Dutch can't help himself, and says just a little too much, further inciting the unhappy offender. When Shane discovers that Aceveda has a list of all the marked bills from the money train heist, Vic and the Strike Team spin a plan to steal it from David's office.
When Vic and the Strike Team fall short of discovering which bills from the money train are marked, there is only one option left - to steal the safe, which contains the list of marked money, from Aceveda's office. The scheme gets interrupted when one of Vic's open cases, which involves a missing girl, is suddenly linked to a Narco Corrido song. The discovery of Narco Corridos, (popular songs in Mexico that depict crimes that have actually happened), gives Vic the blueprints behind several crimes. He must now work with Dutch and Claudette to find the singer and finally close his case. With the help of the Decoy Squad, they finally find the missing girl at her boyfriend's house where she has been hiding out. Meanwhile Claudette takes down a meth lab that is using illegal immigrant women as slave labor. While investigating the crime described in one of the songs, Vic comes face to face with an old fling and sparks fly. Danny and Julien are docked for going off the grid on the Tommy case and are forced to handle the annual inventory that creates some trouble for Dutch when a laptop is missing. David pays a late night visit to his cousin, Rigo's, house. He confesses to Rigo about the rape and Rigo recommends that there is only one way to take care of the problem.
When Trish makes an undercover phone call to the Barn, Claudette discovers that she and Walon are in serious danger. As Claudette enlists the Strike Team's help and Walon is recovered, he reveals that there is a mole in the system that led to him and Trish getting made. Walon claims Claudette is responsible because she failed to read about the mole on a report he filed. With Trish still out there and Claudette at fault, Vic uses the opportunity to create a wedge between Claudette and the Decoy Squad. Meanwhile Dutch works with Danny to make some headway in the "Cuddler" rape case, but the case takes a turn for the worse when an elderly woman turns up cuddled. Vic and his team finally uncover Trish and bring her to safety, but not before she takes drastic measures to keep herself alive on the job. When Tommy realizes David's not going to help him get his job back, he makes a grave decision no one expected. Ronnie reveals that there is k missing from the Money Train stash, causing each member of the Strike Team to question one another.
When Danny and Julien find a young, black graffiti artist lynched at a youth center, David limits the investigation to only Dutch and Claudette. It's not until a Latino priest is killed in connection with the same hug that David calls in both the Strike Team and the Decoy Squad, causing David's superiors to accuse him of racial prioritizing. Vic and his boys are happy to help with the case because it finally gets them back on the streets. Meanwhile, Vic discovers that Corrine's been assaulted by a junkie and when he comes to help, he finds himself face to face with Owen, Matthew's therapist, who has become Corrine's boyfriend and his son's new father figure. Shane also gets dealt a familial blow when the missing money train cash is linked to Mara and her mother. Back on the case, Vic and his team use their brand of "aggressive policing" to solve the murders, discovering the grim truth that rocks Claudette and the community. Danny and Julien wrap up their case when they discover the same perp who robbed and beat up a Hassidic man and his son is the same guy who assaulted Corrine at the hospital.
While trailing Juan and Ricky, the two guys who assaulted him, Aceveda finds himself in a near fatal confrontation during an attempted liquor store robbery. Determined to bring down his rapist at any cost, Aceveda enlists the help of Vic and his guys to find him, dead or alive. Along the way, Aceveda recovers the cell phone that was used to photograph the rape. He also manages to shoot and hug the only other witness to the assault, Ricky. Meanwhile, Claudette rejoins Dutch on the search for the cuddler rapist as they get a stunning break on the case. When Mara reveals what a bloodsucking grifter her mother can be, Shane decides to confess to Vic and the team that Mara stole the money train cash to help her crazy mom. The Strike Team is forced to set up an unsuspecting ex-con by dropping a bag full of marked money in his path.
Vic and the strike team are back out on the streets on a routine bust when a banger takes a shot at Shane. When they shakedown the shooter, they find themselves in the middle of a prescription drug running ring. As they follow that lead, they find something bigger than they expected. Using Danny to go undercover as a soccer mom running drugs on the side, they discover a complex money laundering scheme being run out of a custom car outfit. Meanwhile, Dutch gets the word that Will, the Cuddler rapist, is ready to talk. Will's wife, Joanna, is also waiting at the Barn to talk to Will who completely refuses to communicate with her. As Dutch plays middle man between Will and his wife, he attempts to get inside the mind of a hugger and why he did what he did. Will mocks Dutch's text book analysis and in turn, psychologically digs into Dutch.
Aceveda assigns Vic and his team to serve a high risk warrant to a Korean fugitive. What Vic and his guys think is a regular take down, turns into a dangerous game of cat and mouse. When two children are killed in the crossfire, Vic finds himself in the middle of a hostile struggle with the Korean community who refuses to give up one of their own. Meanwhile, Claudette and Dutch focus on a robbery case involving a woman holding up convenience stores to get cash in order to leave her abusive husband. When their suspect ends up dead, this strikes a chord with Claudette. Julian and Danny are assigned to a stolen furniture case and enlist the help of one of Vic's contacts who knows the stolen goods business from way inside.
When the key suspect in the Armenian money train robbery turns up missing, Aceveda discovers there is a mole in the treasury department who is feeding information to the Armenian Might. Vic and the Strike Team race to find the money train robbery suspect, who they originally framed, in order to keep the cover on their story. With the help of Diagur, the Strike Team finds their man, O'brien, and order him to get out of town before he's brutally cuddled. Meanwhile, the Strike Team realizes that O'brien has ignored their warnings to get lost and is still in town collecting on a sports bet. When they track him down, it's too late, the Armenians have reached him first. They must get rid of O'brien's body so that the Treasury department will continue to consider him the main suspect and investigate his disappearance.
With the deadly Armenian triggerman, Margos, hot on their trail, the Strike Team is turning over Little Armenia to find him first. A chilling discovery is made when the mole in the Treasury department reveals that names and photos of the Strike Team have been delivered to the Armenian Might. As the Strike Team digs deeper into the Armenians, they discover a helpless Armenian woman whose sister is being held hostage by Margos. Meanwhile, Dutch and Claudette investigate the shooting of a public defender after the sentencing of a One-Niner. What they think could be retribution from the One-Niners turns out to be a much more complex hug case as they discover that the public defender has a drug problem and used regularly while she was in court.
When Aceveda confirms that the Strike Team is the target of an Armenian mob hit, Mackey must take matters into his own hands. Meanwhile, Whym's career is on the line when she disobeys Aceveda's orders to put a case to rest that may prove the innocence of convicted felons.