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.

Bodie walks out of detention pretending to be a janitor but Patty is recovering in hospital and is pleased that his injuries will result in a medical pension. Avon Barksdale puts a contract out on Omar and others who robbed him. He wants to make sure everyone on the street knows he's not to be messed with. Judge Phelan keeps the pressure on and Daniels recommends to the Deputy that they need a wire. McNulty suggests they get a warrant to clone the pagers the drug runners use. Det. Fremon is one step ahead of everyone having already found D'Angelo Barksdale's pager number.

Avon, Stringer and Wee-Bey discuss how best to deal with Omar after the attempted hit on Avon, deciding to let him think they want peace, whilst secretly planning to kill him. As such, Omar and Stringer meet for a parley, with security provided by Prop Joe. Meanwhile, Stringer insists on decreasing Avon's visibility in light of the detail's attempt to follow him after the basketball game. An irritable Phelan signs an affidavit for the new phone being used by the pit crew, and Pearlman tells McNulty that he is not up for automatic re-election, possibly because of the feathers he has ruffled due to his involvement with the Barksdale case. D'Angelo tries to understand why Shardene has left him, and after being clean for three days, Bubbles gets some advice from Waylon, before turning to Greggs for support. Meanwhile, McNulty attempts to flip Wallace, and the detail identifies Barksdale's main stash house. However, when Orlando's attempt to purchase weight gets him a lot more than he bargained for, Burrell sees an opportunity for a dangerous undercover operation.

While Greggs' life hangs in the balance, the entire department attempts to hunt down Savino. When Wallace flips, willing to testify that Stringer, Wee-Bey and Bird killed Brandon, Daniels stashes him in his grandmother's house on the outskirts of the city, but he soon becomes restless. Stringer tells Wee-Bey he needs to get out of Baltimore until the Savino investigation cools off, while Avon considers his next move. When McNulty and Pearlman try to pressure Levy into giving up Savino, he proves smarter than they gave him credit for. Meanwhile, when the detail's hand is forced, and a series of city-wide raids are ordered so as to appease Burrell's desire for "dope on the table," McNulty goes to see Phelan for help, but is surprised at his reaction. Daniels decides not to raid the main Barksdale stash house, but when word of his plan gets back to Burrell, he realizes there is a snitch in the detail. Elsewhere, Bubbles finds it increasingly difficult to stay clean.

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.

Detective Jimmy McNulty finds the body of a woman floating in the water while carrying out his new assignment of Harbor Patrol. Major Valchek has his gift to a local parish trumped by Frank Sobotka, his rival in the local stevedores union. And on the waterfront, a shipping container destined for 'The Greek' bakes in the sun with perishable cargo.

Lt Cedric Daniels lets it be known he is going to leave the department. McNulty pursues the identity of the Jane Doe found floating in the harbor. A pair of young longshoremen, Frank Sobotka's son Ziggy and nephew Nick, heist a container and sell its contents, digital cameras, to men working for The Greek.

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.

Trying to let go of police work and return to his marriage, McNulty gives up on identifying his Jane Doe. The detectives look into Sobotka and his money. For his union, Sobotka tries to play the political game. D'Angelo wants to live life outside of Barksdale's umbrella and Bell brings in outside help for the problem.

The detail uses satellite technology to its advantage. Bodie is unhappy that Proposition Joe's people are selling on his turf. Valchek visits the FBI in an attempt to get real results on the docks. Ziggy's deal with Double-G goes bad in a big way. Greggs considers motherhood and Prez makes a major blunder.

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.

Omar continues his bold strikes on the heavily guarded Barksdale stash houses. McNulty launches his own investigation into last year's prison suicide of D'Angelo Barksdale. On the streets the bloodbath continues, prompting Burrell and Rawls to jack up the heat on their district commanders. The street violence also presents Daniels with a tough decision. A beleaguered Cutty tries to get his life back on track.

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.

Poot returns to the corner after a stint in prison--and is welcomed back. Carcetti engages in a testy budget battle with City Council President Campbell, promotes Daniels, and hits a snag in his efforts to relieve Burrell of his duties.

Campbell tries to smooth out the transitions in the police department. The newspaper scrambles to confirm surprising news from City Hall, but lose out to the TV media in scooping a high-profile Grand Jury appearance.