The second season, along with its ongoing examination of the drug problem and its effect on the urban poor, examines the plight of the blue-collar urban working class as exemplified by stevedores (longshoremen) in the city port, as some of them get caught up in smuggling drugs and other contraband inside the containers that their port ships.
In a season-long subplot, the Barksdale organisation continues its drug trafficking despite Avon's imprisonment, with Stringer Bell assuming greater power.
McNulty harbours a vendetta against his former commanders for reassigning him to the marine unit. When 14 young unidentified women are found dead in the port area, he makes a point of proving that they were murdered in his commanders' jurisdiction.
Meanwhile, police Major Stan Valchek gets into a feud with stevedore union leader Frank Sobotka over competing donations to their old neighbourhood church. Valchek demands a detail to investigate Sobotka.
Daniels, having impressed the Major with his work on the Barksdale case, is assigned to lead the detail.
As with the previous season, the targets of the investigations are explored and fully realised as characters. Life for the blue-collar men of the port is increasingly hard and work is scarce.
As union leader, Sobotka has taken it on himself to reinvigorate the port by convincing politicians to support much-needed initiatives. Lacking the funds needed for this kind of influence, Sobotka has become involved with a smuggling ring.
Around him, his son and nephew also turn to crime, as they have few other opportunities to earn money.
It becomes clear to the Sobotka detail that the dead girls are related to their investigation, as they were in a container that was supposed to be smuggled through the port.
They again use wiretaps to infiltrate the crime ring and slowly work their way up the chain towards The Greek, the mysterious man in charge.
But Valchek, upset that their focus has moved beyond Sobotka, gets the FBI involved. The Greek has contacts inside the FBI and starts severing his ties to Baltimore when he learns about the investigation.
After a dispute over stolen goods turns violent, Sobotka's son, Ziggy is charged with the murder of one of the Greek's underlings. Sobtoka himself is arrested for smuggling; he agrees to work with the detail to help his son, finally seeing his actions as a mistake.
However, the Greek learns about this through the FBI and scuppers the case against himself by having Sobotka killed. The investigation ends with the 14 homicides solved but the perpetrator already dead.
Several drug dealers and mid-level smuggling figures tied to the Greek are arrested, but he and his second-in-command escape uncharged and unidentified.
The Major is pleased that Sobotka was arrested; the case is seen as a success by the commanding officers, but is viewed as a failure by the detail.
Across town, the Barksdale organisation continues its business under Stringer while Avon and D'Angelo Barksdale serve prison time.
D'Angelo decides to cut ties to his family after his uncle organises the deaths of several inmates and blames it on a corrupt guard to shave time from his sentence.
Eventually Stringer covertly orders D'Angelo killed, faking it as a suicide. Avon is unaware of Stringer's duplicity and mourns the loss of his nephew.
Stringer also struggles with the loss of his drug suppliers and bad quality product. He again goes behind Avon's back, giving up half of Avon's most prized territory to a rival named Proposition Joe in exchange for a share of his supply.
Avon, unaware of the arrangement, assumes that Joe and other dealers are moving into his territory simply because the Barksdale organisation has too few enforcers. He contracts a feared assassin named Brother Mouzone.
Stringer deals with this by tricking his old adversary Omar into believing that Mouzone was responsible for the vicious killing of his partner in their feud in season one. Seeking revenge, Omar shoots Mouzone, but realises Stringer had lied and calls 9-1-1.
Mouzone recovers and leaves Baltimore, and Stringer is free to continue his business with Proposition Joe.