Baltimore Det. Jimmy McNulty finds himself in hot water with his superior Major William Rawls after a drug dealer, D'Angelo Barksdale who is charged with three murders, is acquitted. McNulty knows the judge in question and although it's not his case, he's called into chambers to explain what happened. Obviously key witnesses recanted their police statements on the stand but McNulty doesn't underplay Barksdale's role in at least 7 other murders. When the judge's raises his concerns at the senior levels of the police department, they have a new investigation on their hands. Lt. Cedric Daniels is put in charge with Kima Greggs as the lead detective. As for Barksdale, he finds himself demoted to a low-level dealer after his arrest and he obviously has to prove himself yet again.

Avon Barksdale is becoming paranoid and thinks he's being watched. He's also worried his phone is being tapped. He also thinks there's a snitch in D'Angelo's crew and he's told not to pay anyone until it's sorted. D'Angelo isn't too pleased when he hears Avon has given Stinkum a new territory. Judge Phelan visits the squad to sign the warrants to clone D'Angelo Barksdale's pager. The numbers they're collecting are coded and don't make much sense. Det. Prez Pryzbylewski figures it out however. McNulty and Greggs try to get information from Omar.

Avon takes care of Omar's man Brandon but Wallace, who saw Brandon in the arcade, isn't too comfortable when he sees what they've done to him. Avon gives D'Angelo and Wallace a bonus for their good work. The police meanwhile get authorization to place taps for the pay phones used by D'Angelo and his crew but can only listen in when one of their suspects is using it meaning they'll have to keep the phones under constant observation. McNulty is in a tight spot when Major Rawls gives him a week to report back to his old job. When he realizes the connections McNulty's made in the various shootings, he announces he's going to arrest the Barksdales for murder and threatens to mess up the drug investigation.

Burrell reluctantly sides with Daniels in the disagreement with Rawls, giving the detail more time to make a case against Avon, despite his fears the operation is beginning to sprawl. McNulty and Pearlman present the detail's findings to Phelan, who signs an affidavit for a further thirty days of electronic surveillance. Using information from the wire on the pit pay-phones, the detail catch a runner on his way to the pit with a re-up. However, they elect not to arrest the driver, Anton 'Stinkum' Artis (Brandon Price), so as to avoid giving up their evidence in the charging documents. Stinkum's apparent free pass from the police convinces Avon and Stringer that their operation has been compromised, and Stringer introduces a new set of operating procedures. Rawls gives Det. Michael Santangelo (Michael Salconi) a choice; acquire information that he can use against McNulty or solve some of the department's open homicides, whilst the owner of Avon's strip club, Wendell 'Orlando' Blocker (Clayton LeBouef), has a proposal for D'Angelo. Meanwhile, Bubbles and Johnny attend an NA meeting, and Bubbles is moved by a speech given by recovering addict Walon (Steve Earle). Investigating the murder of the witness in D'Angelo's trial, with some help from Omar, the detail target Barksdale hitman Marquis 'Bird' Hilton (Fredro Starr).

D'Angelo speaks to Wallace, who tells him he wants to go back to school and get out of the Game. However, Malik 'Poot' Carr (Tray Chaney) discovers Wallace has started using cocaine to help him deal with his guilt over Brandon's murder. Freamon gets Sydnor and Prez started on the complex Barksdale money trail, including possible political connections, and they are surprised to find Avon's corporations have been buying up vacant buildings in run-down parts of the city. Greggs and Freamon approach D'Angelo's girlfriend, Shardene Ennis (Wendy Grantham), who works at Orlando's, in the hopes they can turn her into a CI. After Bubbles narrowly avoids a beating whilst stealing a package that turns out to be stepped on, he decides to try to get clean. Avon and Eastside kingpin 'Proposition' Joe Stewart (Robert F. Chew) stage the annual East vs. West basketball game, but when the detail follows Avon afterwards, they get something they never expected. Meanwhile, having already killed Stinkum, Omar sets in motion a plan to gain revenge on Avon for Brandon's death.

Due to the camera at Orlando's, the detail gather enough information to arrest Avon and many of his people, but, with Wallace dead, they are unable to bring charges against Stringer, who's left on the street. However, disgusted that Avon and Stringer had Wallace killed, D'Angelo flips on the entire organization, giving the detail more information than they could have ever hoped for. As Daniels figures out who the snitch is in the unit, Herc is shocked when he is passed over for promotion in favor of Carver, who scored lower on the sergeant's exam. In Philadelphia, Wee-Bey is arrested and gladly admits to murder after murder. Finally figuring out why Avon has been buying vacant properties in the city, Daniels, McNulty, Freamon and Pearlman take their evidence of political involvement to the FBI. Meanwhile, D'Angelo's mother, Brianna (Michael Hyatt), attempts to convince him to stand with the family.

McNulty goes on a self-assigned moral mission to identify his floater, but his old partner, Bunk, says they have more pressing matter at hand: finding Omar to testify against a Barksdale trigger man in one of last year's murders. To placate Valchek, Burrell asks Daniels to lead the detail investigating Sobotka, and Daniels agrees.

The detail has a setback. Russell and Bunk revisit Philly, looking for evidence. Brother Mouzone talks with Stringer Bell regarding their agreement, leaving Bell to contend with Avon Barksdale. McNulty and Greggs return to the Westside, where they discover new connections. Herc and Carver feel disrespected by fellow officers. Nick tries to come to terms with the Greeks, and himself.

After the notorious Franklin Terrace public housing towers are razed, the Barksdale drug crew searches for a new home on the streets of West Baltimore. McNulty and the detail look to make a case against Stringer Bell with a wiretap on a drug ring run by his ally, Proposition Joe. Daniels' promotion is derailed by City Hall due to his estranged wife's political ambitions.

The brutality at police headquarters continues over the perceived failure of department commanders to rein in the city's crime stats. Another hit by Omar on the Barksdale stash houses goes horribly wrong. Proposition Joe summons Stringer Bell to a meeting and tells him that the cops have screwed up. Daniels reassigns his detail after the wire on Stringer Bell goes dead.

Johnny pressures Bubbles to stop snitching for the detail. Cutty lies to his grandmother about going straight. McNulty realizes pursuing Barksdale and Bell is a losing cause, so he turns his attention to nailing Kintel Williamson. Colvin's free drug dealing zone, now known in the streets as Hamsterdam, scores a small victory. Avon Barksdale emerges from prison to a warm welcome from Stringer Bell.

Daniels goes ballistic when the detail gets reassigned to the Western District. Stringer Bell learns from Donette that Brianna is thinking about talking to McNulty. Bunk receives a gift wrapped surprise. A single cell phone allows Freamon to begin mapping out a communications network for the Barksdale organization. Marlo dispatches a drive-by on a Barksdale drug corner.

The wire begins to yield information about the Barksdale organization. Stringer and Avon reminisce on how far they have come. McNulty finds the way to a key piece of the puzzle in an unlikely place. Awaiting his fate, Colvin works behind the scenes to shape the outcome of Amsterdam, while protecting his men from possible repercussions. Bubbles considers a new partner.

Avon readies his troops for a seemingly endless war against Marlo. The detail works towards the top rungs of the Barksdale organization with the information garnered from the wire. While Royce continues to grapple with Amsterdam, Burrell offers a deal to minimize the fallout. Carcetti's political plans become obvious to his friend and fellow councilman Tony Gray. Bubbles offers his view of the world. McNulty changes tack.