During the trial of D'Angelo Barksdale, a mid-level dealer accused of hug, the prosecution's star witness takes back her testimony, resulting in a not guilty verdict. After the trial, Detective James 'Jimmy' McNulty explains to Judge Phelan how he suspects the Barksdale crew for a slew of related murders. The judge soon contacts McNulty's superiors about this and McNulty is taken to task for his indiscretion. Meanwhile, D'Angelo is free to return to work, but he soon discovers that he's been demoted.
"You cannot lose if you do not play". - Marla Daniels
The witness who testified against D'Angelo winds up being a hug case for "Bunk" Moreland. However, McNulty tells Bunk that since the victim testified against D'Angelo, this hug was probably ordered by Avon Barkdsdale. McNulty and Bunk pick up D'Angelo for questioning and convince him to write an "apology" to the victim's family. Just as he's about to start, D'Angelo's attorney arrives and makes him leave. Meanwhile in "The Pit", Detective Greggs gets some inside information courtesy of Bubbles. New investigation team member Prez arrives with a heavy reputation of incompetence, which worries Lieutenant Daniels. Daniels's concerns are supported when Prez teams up with Herc and Carver to make their own moves in the case by going to the projects to "bust heads" for information. Things backfire and a quasi riot ensues.
"The king stay the king". - D'Angelo
After early morning "field interviews" conducted by Herc, Carver and Prez lead to a minor riot and bad publicity for the police, Daniels gets called in by the Deputy Commissioner. McNulty sends Mahone and Polk to the terrace to get a photo of Avon Barksdale. They come up short but soft- spoken Freamon comes through with an old photo from Barksdale's boxing days. McNulty and Greggs visit FBI agent Fitzhugh to try and obtain some surveillance equipment. D'Angelo delivers the daily count to Stringer Bell who in turn, gives D'Angelo a bonus. Later, while Bodie and D'Angelo wait for the new supply to arrive, D'Angelo offers to get food. While he's gone Bodie, Stinkum and the crew go to retrieve the new supply only renegade dealer Omar and his crew get there and steal the drugs for themselves. The next day D'Angelo gets chewed out by Wee Bey - a Barksdale enforcer - for not being around when the incident happened. After getting chided by his superiors, Lieutenant Daniels mobilizes the team to raid "The Pit". Bodie hits one of the detectives while getting arrested and the rest of the officers proceed to beat Bodie. McNulty secretly meets with agent Fitzhugh who tells him to watch out for Lieutenant Daniels - who might be on the take.
"It's a thin line 'tween heaven and here". - Bubbles
Bodie manages to slip through security and escape from lockup. Meanwhile Herc and Carver continue their renegade ways by travelling to Marlboro to find Bodie and beat him into giving up information on the case. Once they get there, Herc has a change of attitude after meeting Bodie's grandmother. Furious at being robbed of his product during the "re-up", Avon Barksdale instructs Stinkum, Wee-Bey and Stringer to double the existing reward to anyone who eliminates Omar and his crew. When Bodie returns to the pit, he explains how no jail can hold him because he's too tough. He further challenges D'Angelo's mettle by implying that D'Angelo's weak. D'Angelo responds by telling how he killed one of Avon Barksdale's ex-girlfriends after she threatened to give Avon up to the police. AFter hearing this, Bodie becomes cautiously impressed. Sgt. Landsman tells Major Rawls that despite all the screw ups, McNulty's tenacity and obsession with getting the job done usually results in closed cases and that the Major should probably cut McNulty some slack. Detective Freamon discovers D'Angelo's pager number just when Greggs and McNulty figure out a cloned pager could be the advantage they need.
"..a little slow, a little late". - Avon Barksdale
Avon becomes more and more suspicious, he orders Wee-Bey to change phone lines in his apartment and promotes Stinkum to manage a new territory. He gets word that one of Omar's crew members has been "got". Stringer Bell warns D'Angelo that a snitch may be in his camp. The detectives get their affidavit approved for a cloned pager but they are puzzled when the numbers they receive are not regular Baltimore phone numbers.. Herc and Carver catch up with Bodie and attempt to interrogate him.
"..and all the pieces matter". - Freamon
Brandon's bloodied body is discovered in a lot that coincidentally is located next to Poot and Wallace's home. Wallace in turn, reports this to D'Angelo, and tells him about how seeing Brandon's boy has started to bother him. D'Angelo tells Wallace that he needs to get over it, but Wallace is still unsure about all he is involved in. Wallace gets even more unsettled about the situation after Avon rewards D'Angelo and him with extra cash for their parts in getting Brandon taken care of in the first place.
"A man must have a code". - Bunk
Greggs, Herc, Carver, and Syndor grab the runner who is holding the re-up stash for the pit. Now that the cops have the stash, a furious Avon begins to question D'Angelo about a possible snitch in the pit. D'Angelo says it can't be possible and he knows nothing of a snitch. Stringer tells D'Angelo and his crew they are to now use pay phones a block away and to not use the same phone twice. This in turn disconnects all the detective's wiretaps they fought so long to get.
"Come at the king, you best not miss". - Omar
McNulty has his sons play the game of "front and follow" with Stringer Bell as the target at a local market, and the two get Bell's license plate number. As a result, the two get Stringer's license plate number and McNulty couldn't be happier. Greggs and Carver bust a driver picking up a suspiciously large amount of cash from the Towers, only they are forced to return the money on orders of the Deputy Commissioner. Avon finds out about Orlando's inquiries about branching out into "dirty" business, and makes it clear to Orlando that the plan will never happen.
"Maybe we won". - Herc
Freamon gets Syndor and Prez started on the Barksdale money trail. They discover the usual ties to dummy companies, but they also find large sums of political contributions. Herc and Carver bust Wee-Bey holding .000 but only ,000 is reported. Lieutenant Daniels discovers the discrepancy and orders them to find the money before the morning roll call. Omar's mission takes him to Proposition Joe where he promptly offers another recently stolen Barksdale stash to Joe in exchange for Avon's pager number.
"And then he dropped the bracelets..". - Greggs
After being clean for three days straight, Bubbles gets some strong advice from another former addict named Walon. He also gets a promise of extra help from Detective Greggs. When Omar's hug attempt on Avon Barksdale fails, Stringer lays down some new laws for the Barksdale crew. There will be no phone use, no more money runs, a new pager number and anyone that needs to talk to Avon has to go through Stringer first. They also send a word to Omar that a truce will be offered to him. As the team goes through their setup of one of Barksdale's people, one of the officers gets shot.
"Dope on the damn table". - Daniels
While Greggs' life hangs in the balance, the officers deals with the shock in many different ways. Herc, Carver, and Syndor get back on the case after Freamon puts the incident into perspective. After seeing McNulty close to the breaking point, Rawls instructs him not to have any guilty over Gregg's shooting because he's not the one responsible. Daniels is ordered by the Deputy Commissioner to raid all the locations to appease the Commissioner's desire for "dope on the table".
"This is me, yo, right here". - Wallace
After the Barksdale's supply gets confiscated in another bust, Stringer gives more new rules to the crew. Avon and Stringer meet with Levy to discuss the next steps, which include the elimination of any and all persons that can connect Barksdale to the drugs. Wallace goes back to the pit and asks to be let back in but Stringer has another plan for Wallace. Stringer then asks Bodie to take Wallace's old job.
"all in the game..". - Traditional West Baltimore
In the season finale, Greggs finds the strength to finger "Little Man" as one of the men who shot her. Daniels and McNulty go to the feds with crushing evidence about some Baltimore politicians tied to Barksdale, thinking they finally have him. However, the Feds only want the politiicans and not Barksdale. D'Angelo can't swing a deal, and cops to a possession charge and 20 years hard time after a talk with his mother.