With Bolander and Felton suspended, the squad struggles to pick up the slack. Pembleton and Bayliss investigate a body found at a burned-out warehouse and cross paths with arson detective Mike Kellerman, whose theories of the crime put him at odds with the pair. Soon a second building is set on fire, with another body in the rubble. Munch and Howard both sign up for promotion exams.

The department moves into an old bank building when a gas leak forces them to evacuate headquarters. Detectives Lewis and Kellerman partner up to investigate the murder of an old woman; a young news cameraman risks his job to help them solve it. Pembleton is thrown off balance by the change of scenery and the fact that he will soon become a father, while Howard (recently promoted to Sergeant) gets off to a bad start in her attempts to supervise the other detectives.

As Lewis and Kellerman quickly solve a drug-related death, they get a tip on another case: a man who was buried alive in a wall 10 years ago. Munch and Howard target a dealer obsessed with Edgar Allan Poe, relying on psychological manipulation to get him to confess. Munch's stab at a relationship with medical examiner Alyssa Dyer quickly goes sour, and when Pembleton finds that everyone in the office suddenly knows about Mary's pregnancy, he becomes enraged at Bayliss for telling the secret. The department returns to headquarters in this episode.

After a man is killed by skinheads outside a gay bar, Pembleton and Bayliss find their investigation complicated by conflicting information about his sexual preferences. Lewis and Kellerman catch a new lead on Crosetti's last unsolved case, putting Lewis (who originally worked it with Crosetti) and Howard (who took it after his death) sharply at odds with each other. The upcoming Thanksgiving holiday has all the detectives making and rearranging plans on the fly, and Brodie is officially hired as videographer for the homicide unit.

The homicide unit works with the FBI to catch a thrill-killer who is working his way north along Interstate 95. The case takes one strange turn after another, from the detectives' first attempts to profile their suspect until the moment they finally get him in the Box. Giardello's daughter Charisse surprises him by announcing her engagement and plans to move across the country.

Lewis and Kellerman investigate a shooting death at the seedy New Moon Motel on the outskirts of Baltimore. The fact that nearly every tenant has a criminal record, and the victim is missing both a boot and vintage motorcycle, leave the pair awash in potential suspects but short on evidence. Lewis watches the demolition of the housing project in which he grew up, and takes one of its bricks as a memento.

As detectives from Baltimore and New York connect a pair of poison gas attacks in the two cities five years apart, the prime suspect's wife is murdered to keep him from giving up any more information. His son tips off the police, leading to the arrest of an anarchist ex-Special Forces colonel who is trying to start a race war.

This episode concludes a crossover with Law & Order that begins on "Charm City."^[13][14]

Guest star: J. K. Simmons as Alexander Rausch

Lewis and Kellerman are sent to Pennsylvania to pick up Rose Halligan, a fugitive wanted in Baltimore for the murder of her husband. The trip turns into a disaster after she escapes their custody and is later found outside the home of her husband's mistress, whom she has just killed. A case investigated by Munch falls apart in court when Brodie's videotape shows a key piece of evidence missing from the crime scene. Anticipation in the squadroom comes to a head with the announcement that the open captain's position has been filled - and to everyone's shock, it goes to Roger Gaffney instead of Giardello.

Munch and Russert take the case of a retired cop, Edgar Rodzinski, found strangled at his wife's grave. His son Jake is a BCPD detective who knew Lewis from the police academy, and he starts pressing Lewis to give him information and get involved so he can do a little digging of his own. However, his efforts only hinder the other detectives' work. A suspect is arrested and brought to trial; after he is inexplicably acquitted, Jake contemplates taking the law into his own hands.

As Jake Rodzinski struggles to cope with the acquittal of his father's killer, a new case comes in: the killer has been found shot in the head. Kellerman picks up the case and is ordered not to share information with Lewis because of the past relationship between Lewis and Jake. As the evidence increasingly points to Jake's involvement in the shooting, Gee reflects on the changed culture of the police; in the old days, cop killers were shot on sight. Meanwhile, Bayliss nurses a grudge against Pembleton for forgetting his lunch order of a grilled cheese sandwich.

After the detectives learn the name of the man responsible for a long string of abductions and murders, they begin round-the-clock surveillance at his neighbors' house, waiting for him to come home so they can arrest him. As everyone on the shift takes a turn, three topics keep coming up: the personal lives of the homeowners, Giardello's indecision about flying to California for his daughter's wedding, and rumors that Bayliss plans to leave the homicide unit or quit altogether.

A high-profile divorce lawyer is found dead in his own swimming pool, and a man claiming to be his son shows up in the homicide office with evidence to incriminate himself. Pembleton and Bayliss soon find themselves in a face-off with the National Security Agency and a second suspect whose sudden confession seems a little too convenient. Meanwhile, Brodie tries to toughen himself up, Munch buys a VCR of highly questionable origin, and Kellerman tries to unmask the "Lunch Bandit" who has been stealing everyone's food from the office refrigerator.

A young girl is found murdered in a manner very similar to Adena Watson. Remembering how that investigation spiraled out of control, Pembleton insists on working the current case alone and without the usual "red ball" treatment. Bayliss’ conviction that the two cases are connected leads him into a clash with Pembleton and jeopardizes the latter’s efforts to get a confession. Brodie reveals his secret crush on Howard, who thinks he and the rest of the squad are playing a joke on her.

Kellerman becomes the primary on a rash of drug-related killings that prove to be part of a turf war between two rival dealers, "Drak" Fortunato and Luther Mahoney. Each points the finger at the other until a standoff with Drak and a surprise confession convince Kellerman who is responsible for the murders. At a peace vigil attended by the detectives, Drak, and Mahoney, the turf war comes to a sudden end when Drak is shot dead.

Lewis surprises the squad by announcing that he will be getting married at the end of the day's shift, and asks for their help in organizing the reception. Everyone is skeptical, especially Munch, but the wedding turns out to be genuine - and Pembleton's wife Mary goes into labor afterward. Howard's fun-loving sister Carrie comes in from Florence for a visit, prompting Bayliss and Kellerman to vie for her attention. With most of the squad otherwise occupied, Giardello and Howard team up to investigate the death of a controversial talk-radio DJ. After a potential suspect shoots at them and Giardello kills him in self-defense, they learn that a friend of his tipped them off as a practical joke.

Lewis and Kellerman investigate the death of a drug dealer in a housing project, but are hampered by the interference of a private security force run by Black Muslims. The case puts the two detectives at odds with each other and pits Giardello against the bosses, who reveal that nationwide politics may trump the search for the killer. A double shooting in another housing project leads Russert to file departmental charges against the patrolman who responded to the call, arguing that at least one of the victims might have survived if he had not waited to go in. Meanwhile, Munch makes big plans for Bolander's return to work after his suspension, only to have them ruined when the Big Man backs out.

Pressures both on and off the job are mounting for the detectives, as Mary gives birth to the Pembletons' daughter Olivia and Lewis confesses to Kellerman that his marriage is already in trouble. The pair investigate a literal "red ball" case - a man killed by a red bowling ball thrown from a freeway overpass - as Giardello frets over the bosses' upcoming review of his earlier self-defense shooting. Pembleton and Bayliss take a robbery/murder at a fast food restaurant; once they get a suspect in the Box, Pembleton suffers a stroke. He is rushed to the hospital for emergency brain surgery, with uncertain prospects for his recovery.