Season Two of the gritty HBO police drama takes on a new case set against the backdrop of the Baltimore waterfront, where the longshoremen's union struggles to survive in a changing economy.
McNulty makes sure to pay back Rawls for reassigning him to the marine unit by sticking City Homicide with the stone cold whodunit floater he fishes out of the harbor. It's the stevedores versus the police when Sobotka beats out Valchek for the honor of providing a donor-themed stained glass window for the local church. Bodie and Bell take separate business trips, whilst Ziggy makes a fool of himself as Nick negotiates a deal with the Greeks to steal a container from the docks. The Greeks renege on the deal, leaving Russell to discover that the abandoned and broken-sealed container contains the bodies of thirteen women.
After the case gets dumped back in Russell's lap, McNulty offers to help, ensuring that it boomerangs back to Rawls; after Sobotka chews the Greeks out about the bodies in the containers, the Greeks do a little investigating of their own and discover that McNulty's floater was killed by a ship's crewman in front of the other girls, who were then killed to ensure their silence; Brianna urges her brother to take care of business, especially D'Angelo; Valchek strikes a deal with Burrell in exchange for his help in waging war on Sobotka, and Sobotka strikes back by handing the BPD a major embarrassment; Daniels decides to put in his papers; Wee-Bey complains to Avon about his treatment at the hands of C.O. Tilghman; Bunk and Lester are ready to kill McNulty after Landsman puts the fourteen whodunits under their names on the Board.
The non-English-speaking crew of the Atlantic Light proves no help in the investigation, but the first mate unwittingly provides a clue that gets the ball rolling; Nick wonders how he's going to provide for Aimee and their daughter when there's no work on the docks, but rejects Ziggy's idea to make a quick buck by dealing drugs; Omar signs up some new partners in crime; after Stringer discovers that Tilghman is buying from Butchie, Stringer convinces Butchie to give the C.O. a bad package the next time they do business; Sobotka lobbies a state senator whose hands are out; Stringer and Donette reach an understanding of sorts; after Prez spills the beans about the do-nothing task force, Valchek strong-arms Burrell into giving him a real task force headed by Daniels; Avon tries to get Dee's head right with a promise that he won't have to do the whole bit; Ziggy and Nick steal a container and fence the goods to the Greeks; Elena sends Jimmy separation papers.
The medical examiner determines that the bad package which killed five inmates and hospitalized eight others was cut with strychnine, so the heat is on to close the case quickly; as the pressure mounts to deliver Omar's testimony in the Gant case, McNulty enlists Bubbles in the search, but an unhappy Omar finds Bubbles first; Dee confronts Avon about the bad package and washes his hands of the business; Daniels and Burrell strike a deal on the detail, but Rawls refuses to reassign McNulty while okaying Greggs, Hauk and Lester; Stringer continues to struggle with poor quality product from his suppliers; Avon brokers a deal to give up Tilghman for a reduction in his sentence; McNulty continues his efforts to identify his floater; pleased with the outcome of their prior deal, the Greeks come to Nick and Ziggy with a request for bulk chemicals; after Sobotka chews Nick out for stealing the container and tells him to keep a low profile, Nick passes the word to his cousin, which falls on deaf ears; Daniels and Greggs get the silent treatment in their respective homes after they break the news of the new detail to their wives; McNulty signs the separation papers as he asks Elena for another chance; Bunk, Lester and Russell terrify Sobotka when they drop by the bar for a little quality face time.
Ziggy's inability to move a package costs him the Camaro and nearly his life, until Nick intercedes for him; Daniels reaches an understanding with Carver before placing him on the detail; with the help of Bubbles, McNulty delivers Omar to Nathan, who's less than thrilled with her star witness; with Lester transferred to the detail, Daniels gets things moving by sending Herc, Carver, and Greggs out for some hand-to-hands; saddled with Cole, Bunk and Russell end up empty-handed after they haul Sobotka's crew before the grand jury; Russell reaches out to her checker ex-boyfriend and gets information that Sobotka manages to explain away; Nick's dream of home ownership is dashed when Elena, the listing agent for his aunt's house, makes it clear he's priced out of the market; Dee gets a visit from Terrell and Donette, warning her that it's just about business and not to be too impressed with the family love line she's being handed, news that doesn't sit well with Stringer; Bodie has personnel problems in the pit; Valchek lifts a print from the latest picture of the van, which has made its way to San Diego; Stringer gets some advice from his business professor on his supply problem which he passes along to the crew; after The Greek refuses to meet with Sobotka, he calls their deal off, but changes his mind when they triple his fee for each can; McNulty goes to the feds for information on the pross operation but comes away empty-handed when the women refuse to give up what they know without a deal on the table; Ziggy and Nick go surfing and discover that chemicals the Greeks have ordered are used to process coca leaves into cocaine; Daniels agrees to share information with Bunk and Russell, but won't take the bodies without a suspect.
The detail continues to look for the source of the union's money; Omar hands Levy his hat and Nathan a win when he gets on the stand; Nick seeks Vondas's juice in resolving Ziggy's problem with Cheese; abandoning the search for his floater's I.D., McNulty courts Elena, hoping for a reconciliation; Greggs gets a direction on the Russian pross ring from Shardene, and a jealous Cheryl accompanies her and Prez on a field trip to the clubs to follow up Shardene's lead; after spending hours poring over the port's database, Russell finds the pattern they're looking for, but Daniels is still reluctant to pick up those fourteen names in red; Nick gets Vondas his chemicals and agrees to accept half his payment in cash and half in heroin; Stringer's out-sourcing a highly clandestine solution to the problem of Dee's distancing himself from the family and its business has tragic consequences.
Russell goes back in the bag for a day to con Sobotka's crew into thinking that the heat is off; Nick and Frog work out a deal that hinges on an upfront and making good on the money Frog owes Ziggy; as Stringer makes the back end payment to his out-source, it appears that this arrangement may have been all on Stringer; Avon and Brianna are inconsolable, but Donette seems to be taking things in stride; the latest in surveillance technology is no match for the modern urban crime environment and the idiocy of Herc and Carver; Landsman and Rawls are unsuccessful in getting Daniels to take the murders, but Lester finally makes the persuasive argument; after getting a horrifying glimpse of the future during a presentation about robotically-run docks, Sobotka gives DiBiago grease to get some speed under the wheels of union-friendly legislation; depressed that Nick has taken away the package business and made it a success, Ziggy is further demoralized when he becomes the butt of Maui's practical joke; the cloned computer hands the detail the information they need to stake out and follow a stolen can, and thereby connect Sobotka's crew to Proposition Joe; Greggs and Prez continue to follow the pross connection; Daniels tries unsuccessfully to convince Marla that the detail is good for his career; Sobotka asks Nat for another year as union president, as Nat wonders about the source of the contributions Sobotka makes on behalf on the union; Herc and Carver get Nick on surveillance and discuss the merits of creating a phony C.I. to recoup their losses on the bug; taking a break from consoling the bereaved, Stringer discusses a business deal with Proposition Joe, but Avon turns the arrangement down flat; Elena continues to rebuff McNulty's charms.
Sobotka and Nick visit the diner to meet with The Greek. Vondas tries to persuade them to meet with him, but Sobotka is angry and adamant, and only when he begins to leave does The Greek appear. Sobotka explains the reasons for his paranoia and advises that The Greek shut down the warehouse. Instead, The Greek tells him to deliver more disappeared but clean containers there, "to show them there is nothing to hide." When Sobotka demands that he be paid the regular rate for disappearing the clean cans, The Greek is at first reluctant, but then agrees to pay after Nick is insistent.
On the new drug corner they commandeered from their rivals, Bodie and crew sell their repackaged dope, newly named WMD. In an apartment overlooking the scene, a young mother readies her children for school, but soon hits the floor when the rival gang shows up and shooting begins. Both gangs fire wildly, dispersing only when police sirens are heard. Upstairs, the mother discovers that one of her kids has been killed getting ready for school.
The detail uses satellite technology to its advantage. Bodie is unhappy that Proposition Joe's people are slinging on his turf, but business flows anyway. Valchek visits the FBI in an attempt on getting real results on the docks. Ziggy's deal goes bad with Double G in a big way, Greggs considers motherhood and Prez makes a major blunder.
FBI agent Fitzhugh's report detailing Sobotka's plan to flip the next morning in exchange for leniency for Ziggy and Nick reaches FBI agent Koutris, who again tips The Greek to the imminent danger. As Sobotka makes his way to the lonely spot under the Key Bridge for his meeting with Vondas, the FBI agent Koutris sends a message to The Greek and warns him of Sobotka's intention to tell the police what he knows. With Sobotka in sight, The Greek tells Vondas that the union leader must not leave their meeting alive.
Sobotka's woes are finally submerged; Fitzhugh realizes his messages weren't reaching their intended target; Nick trades information about The Greek for a soft place to fall with the Feds.