Lt. Daniels puts his team together but the extra help he's asked includes several less than stellar officers. It also includes McNulty, who is obviously in the doghouse. When one of the witnesses against D'Angelo Barksdale is found dead, McNulty and his homicide partner 'Bunk' Moreland bring him in for questioning. They have no evidence that he had anything to do with the killing but their instincts tell them otherwise. When news of the witnesses death hits the press, Major Rawls is convinced that McNulty is again responsible. Three of the newly assigned detectives, Hec, Prez and Carver decide to go to the towers and flex a little muscle only to have it turn into a major disaster.

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).

McNulty uses his children to tail Stringer after a chance encounter in a local market, with one of them getting his license plate. As the detail discuss the implications of the pit pay-phones being disconnected, speculating the crew are going to start using phones outside their immediate area of operations, Herc and Carver prepare for the sergeant's exam. Stinkum, Roland 'Wee-Bey' Brice (Hassan Johnson), and Savino Bratton (Chris Clanton) raid Omar's pad, but he is nowhere to be found. Avon is unhappy when he learns of Orlando's proposal to D'Angelo. Meanwhile, Greggs and Carver arrest a driver picking up a large amount of cash from the towers, but are surprised to learn he is an aide to State Senator Clay Davis (Isiah Whitlock Jr.). Burrell is furious with this turn of events and confronts Daniels about the direction in which the case is heading, giving him one week to charge Avon and/or Stringer. Phelan, however, tells Burrell he wants the full thirty days of surveillance assigned by the court. As Wee-Bey and Stinkum attempt to take over new territory, they encounter an unanticipated problem.

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.

Major Valchek gets back at Sobotka for the church gift fiasco, and a feud begins. Avon Barksdale continues to run his empire from a prison cell. On the waterfront, Port Police Officer Beatrice Russell gets stuck investigating the contraband in the The Greek's container. McNulty lends a hand with the investigation.

Greggs and Prez tap into the circuit of Russian prostitutes. With two sets of evidence, the detail goes to Pearlman who tells them neither crime merits a wiretap, but a drug connection could give the case legs. Rawls can't persuade Daniels to take the murders, but new evidence does. Though discord grows in Barksdale's empire, Bell tries to hold it together.

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.

Greggs and McNulty recruit Bubbles to gather street intelligence on the Barksdale gang. Cutty seeks out the Barksdale gang after he loses his taste for the straight life. Bunk feels the pressure to find Dozerman's gun. Daniels worries that Avon Barksdale, having cut a prison deal, will be paroled. Stringer Bell tries to make amends with Donette.

Major Colvin instructs his men to use brute force to get the message out to street dealers about his free zone. Avon Barksdale and Stringer Bell discover that real estate development has its own pitfalls. McNulty and Greggs ask Daniels to let them renew the Bell and Barksdale investigation. On Barksdale's orders, Cutty plans to take back corners from Marlo's crew.

Responding to an officer's call for help, McNulty and Prez turn up the wrong alley with unanticipated results. Cutty is surprised to find help from within Baltimore's power structure for his proposed boxing gym. Omar decides to go it alone against Avon Barksdale and Stringer Bell. Bubbles is wired up and sent into Hamsterdam

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.

With his lead dwindling, Royce resorts to extreme measures to stall Carcetti's momentum. At Bodie's corner, Michael proves adept as a runner, with Bodie and Marlo taking notice. A re-up bodega is put under surveillance by Omar and Greggs.

With Freamon and Greggs moved to Homicide, Herc and Dozerman join Marimow in the stripped-down Major Crimes Unit. Cutty gets a 'custodial' job at Tilghman School mopping up truants, but can't make headway in his efforts to mentor Michael.

Carcetti's master plan for the police department is leaked to the press, sending the brass into a panic. Marlo turns to Proposition Joe to help with an enviable problem. Whiting and Klebanow drop a bombshell on the newspaper staff.

Carcetti maps out a damage-control scenario with the police brass in the wake of a startling revelation from Pearlman and Daniels. Their choice: clean up the mess...or hide the dirt.