The middle school gunman demands that his pet pig be brought to him, then shoots and critically injures a female student and sets the classroom on fire after the police fail to do so. After the hostages are rescued and he is taken to the hospital with severe burns, the squad connects this incident with Mrs. Uba's murder and realizes that her son Gerry committed both crimes. The injured student dies, and Gee is furious when Danvers initially holds off on charging him with multiple first-degree murder charges because the state will save money by waiting to charge the incapacitated perpetrator. Meanwhile, Danvers gets engaged, Pembleton stops taking his medication after discovering its effects on his mental focus and sexual relations with Mary, and Munch learns that Brodie has been evicted and offers to let him move in.

At the state penitentiary, a cafeteria scuffle turns into a riot that leaves two inmates dead. The whole squad (except for Pembleton) starts to investigate, but no one - including several killers apprehended in previous episodes - is willing to provide any information. Bayliss concentrates on inmate Elijah Sanborn, trying to use the news of his son's recent arrest as leverage to get the facts, but the truth only comes out after a second assault occurs in the prison. Meanwhile, Pembleton begins target practice in hopes of qualifying on the firing range so he can return to full duty.

Guest stars: Charles S. Dutton as Elijah Sanborn, Dean Winters as Tom Marans

Drug addicts all over Baltimore are dying from a batch of adulterated heroin, sold by a dealer in competition with Luther Mahoney. After the dealer is found murdered, narcotics detective Terri Stivers works with the homicide unit to build a conspiracy case against Mahoney and cut off the supply of bad drugs at the same time. The case falls apart when the only witness, Stivers' informant, is also killed. Kellerman is put on desk duty after the entire arson unit becomes the target of a federal investigation for corruption. Pembleton fails his firearms test and begins taking his medication again, and Brodie moves in with Bayliss after Munch throws him out.

Dr. Julianna Cox arrives in Baltimore to begin work as Chief Medical Examiner and look after her ailing father, who soon dies of non-natural causes. The FBI begins to question the Arson Unit detectives as part of the corruption investigation, setting Kellerman's nerves on edge. As Bayliss and Lewis probe the death of a prostitute, a homeless man quickly confesses to both her murder and that of a second woman whose name never appeared on the Board. With help from the detectives, Cox learns that one of her staff members deliberately mis-classified the earlier death as an overdose, then fires him. Bayliss throws Brodie out, whereupon he moves in with Lewis and inadvertently touches off an argument that may end his marriage.

Guest star: Edward Herrmann as FBI Agent Thomas Pandolfi

At a support group meeting for family members of murder victims, three of the squad's cases are described: a carjacking in which a young mother is shot (worked by Lewis and Munch), a brawl at the Waterfront that leaves a man dead (Gee), and a teenage girl found strangled and dumped in an alley (Bayliss). Gee and Bayliss both close their cases, the latter with Pembleton's help. Cox arrives late and reveals that while her father was suffering from a terminal illness, he actually died of injuries when he was the victim of a hit-and-run car accident.

Lewis and Bayliss work the murder of an African-American student at an exclusive, nearly all-white prep school. The case takes a political turn when their focus shifts to an arrogant, manipulative student whose mother is a hardline Baltimore court judge. One of the victim's roommates confesses to the crime, but the detectives continue working to uncover the rest of the facts. Reinstated to full duty after a successful firearms exam, Pembleton wonders if he can trust himself to enter the Box again. Kellerman meets Cox for the first time, offers Brodie a place to stay on his boat, and learns that several members of the arson unit have agreed to testify against him--even though they all were corrupt and he was not.

With Bayliss as primary, Pembleton takes his first case since returning to duty: the murders of a woman and her two sons in their own home. The detectives have different theories about the case, with Pembleton favoring the woman's boyfriend and Bayliss focusing on her ex-husband. They have trouble following each other's leads, but eventually work together in the Box to catch the killer. A witness at a drug dealer's shooting points Lewis and Munch to Junior Bunk, Luther Mahoney's nephew, who readily incriminates Mahoney but is then intimidated into recanting his statement. Brodie gets evicted from Kellerman's boat, then tries and fails to talk both Gee and Russert into giving him a room. Kellerman receives a grand jury summons and spends the night with Cox.

Guest star: Mekhi Phifer as Junior Bunk

When Danvers' fiancee is killed in a bridal shop robbery, Pembleton takes the case, his first as primary since his stroke. Danvers meddles in the investigation and insists that it be assigned to another detective, but Gee refuses to do so. A suspect is brought in and interrogated, then hangs himself after a distraught Danvers confronts him. Cox tells Kellerman that she does not want a relationship with him, sending him into a depression that only lifts somewhat after he learns that the grand jury has been postponed. Gee learns that there will be no high-level support for his detective, and also that an incompetent racist like Gaffney was promoted to captain over him as a reminder of his past failure to support the department. Brodie is thrown out of the morgue after sleeping there overnight.

Brodie takes advantage of an unexpectedly quiet New Year's Eve to present the detectives with a documentary he has made on the inner workings of the homicide unit. The film reveals facts that everyone would prefer to keep private, including a case in which the killer has some bizarre personal habits, and captures a foot chase that runs right through a film shoot headed by director Barry Levinson. The identity of last season's "Lunch Bandit" is exposed - none other than Gaffney - and Cox and Kellerman decide to try to start a relationship. Brodie shocks the detectives with news that he has sold the documentary to PBS as the clock strikes midnight and the phones begin to ring.

Elizabeth Wu, the new police reporter for The Baltimore Sun, becomes an annoyance to the homicide unit as Pembleton investigates the case of an off-duty police officer killed after a drug buy. After she mistakenly destroys the victim's reputation and leads the detectives to her source (who turns out to be the shooter), Barnfather takes advantage of a press conference to get her thrown off the police beat. Meanwhile, Kellerman gets an unwelcome surprise visit from his two delinquent elder brothers, who are on the run from bookies in Cleveland and have stolen Babe Ruth's Baltimore Orioles uniform to pay off their debt.

After a man is found dead in the apartment of one of Brodie's graduate school classmates, Munch is ready to write it off as a suicide, but Brodie refuses to let him drop the matter. Munch and Howard investigate further and, with Brodie's help, lay a trap that exposes the classmate as a murderer. Kellerman and Bayliss uncover the connection between a pair of bombing deaths - the trial of the man who killed the Korean shopkeeper in "Have a Conscience" - and race to stop the perpetrator from completing a campaign of revenge against those responsible for his acquittal. Marriage counseling for Pembleton and Mary only leads to worsening arguments between them, and after he misses Olivia's baptism, Mary takes her and moves out.

Charlie Flavin, the man who shot and blinded Officer Chris Thormann four years ago, has become eligible for parole, and the news has left Thormann unable to think about anything else. His wife and Lewis try to help him past this moment; at the parole hearing, Thormann makes a statement that results in Flavin being put away for another five years. While investigating the death of an abusive husband at his daughter's hands, Bayliss and Pembleton sharply disagree over the question of whether abuse victims deserve any blame for not leaving their abusers. Bayliss later confronts the uncle who molested him as a child; the uncle is disabled and barely able to speak, but Bayliss asks him "Where do I put my hate?". Kellerman spends time with Cox and reveals that he had been considering suicide.

The death of a Nigerian drug courier brings the homicide and narcotics units together in a plan to smash Luther Mahoney's organization. Mahoney shoots one of his own men and a bystander in a panic and is then killed by Kellerman under questionable circumstances, with Lewis and Stivers also on the scene. All three write up the incident as a case of self-defense. An ex-convict calls Munch with information on an old murder; this turns out to be a ruse so he can find the "victim" and kill him. Bayliss agrees to re-partner with Pembleton, then slips out without telling anyone to take care of his uncle.

A murder suspect fleeing from police takes shelter at the headquarters of the African Revival Movement. Interference by both Barnfather and Gaffney leads the unit to realize that someone is pulling strings to stall them. That person is ARM leader Burundi Robinson, who initiates an armed standoff when the police try to serve an arrest warrant. He tells Gee about his time on the force, serving with Deputy Commissioner Harris and losing his job due to Harris' misconduct after a drug bust. Robinson and 15 ARM members commit suicide before they can be apprehended, and Gee promises to expose Harris' illegal acts. Bayliss is nowhere to be found until the standoff is nearly over, and Stivers voices her worries about the Mahoney shooting to Kellerman and Lewis.

Pembleton responds to a shooting call and is shocked to find that the victim is Beau Felton, who has apparently committed suicide. Auto Squad detective Paul Falsone visits the squad room and voices his theory that Felton was leaking information to a car theft ring he was trying to bust. Cox's autopsy reveals that Felton was in fact murdered, and Gee learns that Stuart Gharty (now a detective working in Internal Investigations) sent Felton into the ring undercover to find the leak--a fact that enrages Howard, who remembers how his previous cowardice resulted in the deaths of two men and had hoped he would retire from the BPD. Russert returns from France to help with the investigation. Lewis tries to settle Stivers' mind over the Mahoney shooting, and Pembleton finds out that Bayliss has been taking care of his uncle in order to forgive him. Kellerman and Cox spend another night together. Giardello ignores Gaffney's insults over Harris' resignation, recognizing them as scared bluster from the captain.

Gee brings Falsone and Gharty in on the Felton murder, irritating the rest of the detectives at first, but Pembleton relents somewhat after Gharty reveals that he took a beating while serving an arrest warrant to prove he was no longer a coward. Howard and Russert are taken off the case so they can plan the funeral, since they are both too emotionally involved. Falsone and Gharty realize that they have been using the same informant, who brought Felton into the car theft ring, then blew his cover and set him up to be killed by its leader. By the time the unit raids the hideout, though, everyone in the ring has disappeared. A hung-over Kellerman argues with Cox and annoys Lewis by losing track of a witness for a case they are working. Pembleton reconciles with Mary, now six months pregnant, and she agrees to move back home. After a ceremony in Felton's honor, Gee learns that the department is starting a rotation program that may scatter his detectives.

Guest stars: Jon Seda as Det. Paul Falsone; Peter Gerety as Det. Stuart Gharty; Scott William Winters as Eddie Dugan; Isabella Hofmann as Det. Megan Russert; then Baltimore Mayor Kurt L. Schmoke as himself; then Governor of Maryland Parris Glendening as himself.