Kima Greggs awakens in her hospital bed to find detectives Bunk Moreland and Ray Cole waiting to talk to her to ask for her help identifying her shooters. Bunk shows her photo arrays and she is able to pick out Little Man but not Wee-Bey Brice. She says she could not see the second shooter because he was outside in the dark. Bunk tells her that they have DNA evidence linking the discarded hoodies to Wee-Bey, a page from Wee-Bey to Stringer, and Little Man's prints on a can found near the payphone used for the page. Bunk tells her that the downside is the lack of guns or eye witnesses. Bunk tells her an ID will play easier at trial but Greggs insists that sometimes things have to play hard.
Detective Thomas "Herc" Hauk phones in to say that he has found all of the Barksdale dealers he had warrants for apart from Wee-Bey. Ronnie Mo is one of the dealers being loaded into the prisoner transport. Prez updates the detail's notice board to reflect Herc's arrests. Lieutenant Cedric Daniels worries that their case is about to be shut down unless they can provide new leads. Detective Jimmy McNulty suggests they go behind their superiors' backs to take the case federal. ASA Rhonda Pearlman calls and tells McNulty that D'Angelo Barksdale is being represented by a public defender. The detail realises the rift between D'Angelo and his family and move to interview him.
Avon Barksdale and Stringer Bell meet their lawyer, Maurice Levy, in a parking garage. Avon suggests that there have been too many arrests for a single informant and Levy agrees that a wiretap or other surveillance is more likely. He asks when Avon spoke to D'Angelo about the New Jersey drug run and Avon realizes it was a mistake to have used the office at the club. Stringer says that they must bail out their people despite the downside of showing a lot of cash because otherwise they risk making enemies. Levy hands Avon a phone message from Wee-Bey and asks him about D'Angelo's state of mind. Avon insists that D'Angelo can be trusted, as he is family. Levy suggests that they should consider a structured plea where they give up their own people to avoid sentencing.
McNulty and Bunk discuss Greggs's recovery. Bunk urges McNulty to visit her, telling him that it is about her and not him. Bunk relates the story of Greggs refusing to deviate from the facts and McNulty calls her "real police". Pearlman frostily delivers a tape recorder for McNulty, but has a smile for Bunk. Bunk asks McNulty about their feud and McNulty says he does not know what he has done.
Stringer and Avon relocate to their funeral home business. Avon is initially unsure, but when he sees pallbearers playing dice in the alley outside he reconsiders. Stringer is still paranoid about listening devices. Brianna arrives and they move the discussion outside. Avon asks Brianna to visit their supplier Roberto to get more product and to talk D'Angelo around. When he says that he is sorry for sending D'Angelo alone and promises to make it up to his nephew, Brianna insists that he will.
Pearlman meets with D'Angelo and his lawyer. They discuss a deal based on D'Angelo admitting his involvement and giving them information about murders. McNulty shows D'Angelo photographs of the bodies of Nakeeska Lyles and Wallace. D'Angelo cannot look at the pictures. They also have a photograph of Orlando. McNulty plays a tape of Poot Carr discussing Wallace's drug habit. Next they give D'Angelo a picture of Brandon Wright's body. D'Angelo admits his and Wallace's involvement in identifying Brandon and the link to Stringer. He also relates his recent discussion with Stringer and Avon about Wallace and his guilt over not doing more to protect him. McNulty shows him photos of Wee-Bey and Little Man as the shooters in Orlando's murder. He gives up Wee-Bey's hiding place in Philadelphia. Finally they show him a photograph of Deirdre Kresson and Bunk taps on the desk. Contrary to the tale he told to his subordinates, D'Angelo says that he was not responsible for the murder and that his uncle "played him" over her killing. He says that he delivered cocaine to Deirdre and Wee-Bey drove him. Deirdre told him that she was going to put the cocaine "on ice" which prompts Bunk to say "refrigerator". D'Angelo says that Wee-Bey was the one tapping on the window and shot Deirdre when she moved from the fridge to look out of the window. D'Angelo finishes by telling them that he was born into the drug business. His grandfather was Butch Stanford, and his whole family is involved. He says that he felt more free in jail than at home. He asks for a chance at a fresh start.
Daniels discusses their progress on the phone with Pearlman and excitedly tells his wife, Marla, the news. She hopes that this will square things with Deputy Commissioner Ervin Burrell. Daniels tells her of his plans to reach out to the FBI. He wants to avoid Burrell because he knows about an old FBI investigation into the Danielses' excess funds. He guesses that Burrell does not want to use the information because of the bad publicity it would generate. Pearlman and McNulty discuss their success on the way back to Baltimore. Pearlman calls it a career case and agrees that they should take it federal. When McNulty starts to apologize, she immediately initiates sex in the middle of the police headquarters garage.
Detective Lester Freamon visits a retired colleague from the pawnshop unit, Roy Brown, now working for a phone company. He is there with Bunk to try and track down Wee-Bey in Philadelphia by tracing numbers that have called Levy's office from the city. When Freamon mentions it is connected to Greggs's shooting, Brown is eager to help.
Stringer orders the delivery of a new package of narcotics and learns that there were no problems with the delivery. He meets with one of the few remaining lieutenants and instructs him on how to prepare the drugs and spread the word that their business is open once again.
Later, McNulty meets with Special Agent Terrence "Fitz" Fitzhugh to discuss bringing in the FBI. Fitz is reluctant because the Bureau is not looking for drug cases and he is dubious of Daniels's involvement, knowing that the FBI has investigated him for possible corruption. McNulty vouches for Daniels, saying that he has shown heart in running the Barksdale case. Fitz organizes the meeting and his supervisor, Amanda Reese, is impressed with the case, but says the Bureau is focused on terrorism and corruption. Daniels tells them that there are aspects of political corruption involved also, this prompts them to take the case to the US attorney's office.
In the pit, Bodie organizes the dealers to chase off an independent crew led by a dealer named "Onion". Detectives Ellis Carver and Herc watch from their car, and Carver tells Herc that they will never win because the dealers face beatings over failure, while the cops will get pensions.
McNulty finally visits Greggs' bedside and finds Cheryl sitting with her. Greggs asks about the Barksdale case and McNulty begins to tell her about D'Angelo. Cheryl angrily leaves the room and Greggs tells McNulty that Cheryl wants her to quit. She asks for his advice and he agrees with Cheryl that the case is not worth her injury. She chastises McNulty for waiting so long to visit and, near to tears, he admits that he felt somehow responsible for her shooting. She tells him that the only choice she regrets is not putting enough tape on her gun. He apologizes to her and she asks him to visit Bubbles.
McNulty delivers money to Bubbles from Greggs to help in his fresh start, but finds that Bubbles is using again. Bubbles tries to return some but cannot resist taking it all. He asks McNulty not to tell Greggs that he is using.
Later at the detail, Herc receives notification that he is no longer in line for the sergeant promotion and that Carver has been moved up the list. He is depressed and feels his brutality complaints will keep him from making sergeant, but congratulates Carver anyway.
Brown from the phone company calls the detail with the number for Freamon.
Freamon, Daniels, and McNulty meet with the FBI and the First Deputy US Attorney. Freamon explains the Barksdales' property scam: they have been buying property based on the advice of the politicians they have bribed in areas set for redevelopment and then selling it on at a higher price. The FBI hopes to use the drug dealers as co-operators to target the politicians. McNulty is enraged that they would consider letting Bell and Barksdale reduce their sentences. Daniels ends the meeting, saying they are moving in different directions. McNulty cannot restrain himself and accuses the FBI agents of being empty suits who are ignoring the death of West Baltimore.
Brianna visits D'Angelo in prison. D'Angelo complains that his treatment is not right. Brianna tells him that Avon would take the majority of the punishment if D'Angelo was able to step up and take over. D'Angelo admits that he does not think he will ever be ready to do that. He tells his mother that he has a chance to get out. Brianna tells him that hurting Avon will hurt the whole family, including D'Angelo's son. She tells him that his charge is part of "the game" and without "the game" his family would be destitute. She questions how he is going to start over without his family.
The detail prepares to travel to Philadelphia to arrest Wee-Bey.
Daniels calls Carver into his office and accuses him of acting as Burrell's insider in the unit. Daniels noticed that Burrell was unable to anticipate his actions when Carver was away for training. Carver admits his involvement and says he felt unable to refuse Burrell because of his rank. Daniels warns Carver that now he is a sergeant people will look up to him and if he continues to act in this way he will influence the men under his command to do the same. He ends by saying that Carver must decide whether it is about him or the work.
After the meeting he gives Prez his gun and badge back, Prez is reluctant to leave the office and Daniels dryly jokes about his light trigger pull. When they reach Philadelphia the detail set off Wee-Bey's car alarm to draw him out and make a clean arrest.
Major William Rawls meets with McNulty and congratulates him for the case. He reveals that the First Deputy US Attorney phoned Burrell to complain about McNulty's behaviour in their meeting, tipping Burrell to the fact that the detail had tried to take the case federal. Rawls tells McNulty he wants to see him land okay and asks where he does not want to go - the same question that Freamon had previously warned McNulty about.
Pearlman has a celebratory lunch with her colleague Ilene Nathan. Her mood is broken when she finds out that Levy is now representing D'Angelo. She later meets with Levy to discuss the case. He tells them that the dealers will largely plead guilty for fixed sentences. Avon will likely see a short sentence for attempted possession. Levy offers Wee-Bey to admit to several murders to avoid the death penalty, but insists he acted alone. In terms of asset forfeiture, he offers only the assets linked to the detail's case, leaving out most of the property and the funeral parlour.
At the court hearing, Pearlman presents Avon's guilty plea in exchange for a sentence of seven years. D'Angelo is also present as a defendant. Stringer and Brianna are in the court as spectators, as is McNulty, who cannot bring himself to stay. Pearlman next makes the case against Ronald "Ronnie Mo" Watkins, asking for a fifteen year minimum sentence for conspiracy to distribute narcotics.
Stringer congratulates McNulty on his way out of the courtroom, repeating the phrase that McNulty had muttered to Stringer after D'Angelo's exoneration in the first episode: "Nicely done". Phelan also congratulates McNulty, who is now completely despondent. Finally, Pearlman brings the case against D'Angelo and McNulty returns to the court. D'Angelo's sentence is the maximum allowable: twenty years.
Daniels bumps into Cantrell, now a major, having received the promotion that Daniels had been in line for. Cantrell offers Daniels a move into his new district. Back at the narcotics division Herc is holding an induction for two new detectives. Daniels is amused that his attitude has changed and that he now hopes to make big cases using intelligent investigative techniques. Rawls introduces Freamon to his homicide unit.
Bodie organizes trade in the towers through his new subordinate "Puddin", bemoaning Roc Roc's slowness with his "re-up". Poot oversees the trade in the pit and repeats the speech D'Angelo once gave Wallace about keeping the cash and drug transactions separate to a new dealer named Dink.
Meanwhile Bunk, Ed Norris, and ASA Nathan interview Wee-Bey. Bunk states that they have linked the same weapon to the murders of Deirdre Kresson, Taureen Boyd, and Roland Leggett. Brandon Wright and John Bailey have also been linked to Wee-Bey. Wee-Bey refuses to give up any information on Avon and Stringer. His lawyer recommends he give up all of his crimes to avoid being prosecuted for them later. He admits to killing Little Man and tells Bunk where to find the body. He also admits to killing Nakeesha Lyles and claims to have killed William Gant in an effort to protect Bird. Bunk reports Wee-Bey's confessions to McNulty and the two discuss his false confession about William Gant. McNulty and Bunk know that Wee-Bey's story does not match the facts of the case. As the convicted Barksdale dealers file out of the court room, McNulty once more asks, "What the fuck did I do?"
The season ends with a montage showing: Bubbles and Johnny back on the hustle and Santangelo on patrol in the Western; Burrell promoting Carver; Prez clearing the details board; Greggs gazing wistfully at a car chase from her hospital window; Freamon and Bunk delivering a bottle of whiskey to McNulty at his new post with the marine unit; Stringer overseeing the counting of his profits at the funeral parlour; prolific drug trade throughout the whole of Baltimore. Finally we find Omar, in the South Bronx, NY, holding up another dealer and telling him that it is "all in the game".