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.
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.
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.
Weak product in the pit has Bodie getting heat. Homicide detectives hand out grand jury summonses to stevedores involved in the homicide case, and Port Police Officer Beadie Russell works the lingering affections of an old boyfriend to find out how cargo disappears from the docks.
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.
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.
McNulty goes on a drunken binge of legendary proportions. Fellow stevedores convince Ziggy to fight Maui. Bunk, seeing McNulty's desperation, talks Daniels into asking for him. Daniels does so and Rawls, who has no choice, agrees. After some labor, the wiretap is up, just in time to catch another disappearing container.
Bodie's disastrous sales efforts result in a tongue lashing from Stringer Bell. Ziggy pulls Johnny Fifty into a new caper that makes the Greeks pay big money. McNulty goes undercover in a brothel. As Valchek fumes over the change of targets and Burrell pulls the rug from beneath him, Daniels and Pearlman maintain their composure.
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 makes a desperate move. Nick's deceit is in the open, as Sobotka is overwhelmed by bad news. The Greeks confidently ease out of a brief encounter with the detail and Omar's suspicions are validated. The detail hopes to find Vonda's boss. Nick hopes to repair relations with the Greeks and Sobotka is forced to make a difficult choice.
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.