Bolander and Felton are suspended for 22 weeks without pay for incidents related to activities at a police convention in Washington, DC. Howard plans to take the sergeant's exam. Pembleton and Bayliss are assigned to investigate the death of a body found at an arson. At the scene they meet an arson detective that clashes with Frank's working style. Frank hesitates chasing a suspect, and later we learn that his wife is pregnant. Munch also decides to take the exam, and when the wagering begins on who is going to pass, everyone favors Howard. While the detectives are debating whether the fire was set to cover the murder, another fire is started.

The fire investigation continues. Bayliss' back is acting up and Kellerman is paired with Pembleton. Kellerman shows Gee something, so he is offered a transfer into the department that he first rejects. Kay takes the sergeant's exam, Munch misses it due a ""comedy of errors.""

A gas leak causes the detectives to evacuate the building, so they relocate to an old bank building. Lewis is paired up with Kellerman on the murder of a woman. Sergeant Howard tries to carve out a place for herself with the other detectives, but her efforts prove unpopular. Pembleton has trouble adjusting to the new surroundings and his wife's pregnancy. A cameraman who was at the scene of the murder has who he thinks is the perpetrator on tape; however, when he brings the tape to Gee, he is thrown out before he can say why he's there. The cameraman eventually strikes a deal with Lewis and Kellerman.

The squad returns to the station. The FBI joins with the detectives to stop a ""thrill killer"" who's working his way north on I-95. Gee tries to reconcile with his daughter. The killer smells a rat at a roadblock so he bails out of his pickup. Everyone mobilizes to find him and when they do, the suspect in custody, while identical to the killer, claims he is innocent.

Pembleton and Bayliss investigate a murder that was committed in a gay neighborhood by skinheads and the victim's sexual preference is questioned. Brodie is hired by the department to videotape the detectives' crime scenes. A voice stress analyzer is brought in for a demonstration. Meldrick gets a lead and closes an old Crosetti case that even Howard couldn't crack; it causes a little tension between them.

Technically it's not a homicide; however, Pembleton and Bayliss investigate the ""murder"" of a small boy who's the victim of a stray bullet, which makes him brain dead. The parents must choose what to do with their son. The Pope is in town.

Lewis and Kellerman interview a suspect and uncover a 10-year-old crime, which is assigned to Howard and Munch. Tim lets Frank's secret about Mary's pregnancy slip out. Howard and Munch find the body from the 10-year-old murder bricked up in a wall. John has a date with Alyssa, the ME, but finds himself in bed with her new roommate before their date, so he begins avoiding her. Howard and Munch's murder suspect has a fascination for former Baltimore resident Edgar Allan Poe. Munch plays up that angle while trying to break their suspect.

Jay Leno stops by the Waterfront Bar while in town visiting his cousin Mary; Munch and Bayliss don't want to bother him. A new year starts out with a clean board and Brodie begins his work taping with the detectives. A sniper takes the city hostage, threatening to and executing people every 8 hours. The sniper uses Hangman as a way to leave clues for the detectives. Bayliss is the primary and his back is giving him trouble as he worries about surgery his doctor wants him to have. To combat the pain, he keeps taking muscle relaxants. A suspect is found and cornered and he shoots himself before they can take him into custody. Russert gets demoted when Barnfather doesn't like the way she handled the investigation.

The sniper continues the shootings and everyone returns to duty lacking sleep. The media starts to make their presence felt. Munch begins to worry about Howard's safety, fearing she'll be wounded again. Frank makes his wife wear a bulletproof vest. Gee asks for Russert's help even though Barnfather had ordered her to stand down during the rest of this investigation. A man at the scene of both of the day's shootings is put into the box for questioning. Russert has a talk with the suspect with the subject being keeping people's attention and respect.

Gee is sent upstairs to see Barnfather and everyone speculates about the vacant Captain's position. Lewis and Kellerman are sent to Pennsylvania to extradite a woman back to Baltimore where she is a suspect in the murder of her husband. Munch tries to find a videotape in Brodie's pile. Later after reviewing the tape, they discover a key piece of evidence isn't contained on the tape. Munch wants the tape erased, but Brodie delivers the tape to court and that results in the outcome Munch feared. On the trip back from Harrisburg, Kellerman convinces Lewis that they have time to stop at Neptune's Castle and they lose the suspect, for a moment. Later they lose her again but find her at the house of her dead husband's mistress, delivering a hat. Much to everyone's surprise but not the viewers Gaffney is promoted to Captain over Gee. Captain Gaffney lays down the law.

Lewis and Kellerman try to subdue a large man who's gone on a rampage. The large man is finally subdued and they find him digging up his mother. This case brings out some information about Meldrick's family, and he tries to see his brother, who doesn't want to see him. Kay tries to keep the identity of her new boyfriend a secret, mainly from John, which drives him crazy. Pembleton and Bayliss investigate the death of a man whose body is found in a car. Scheiner says he died from internal bleeding, not the gunshot wound to the groin he was treated for at an emergency room earlier that day. They discover that the doctor may have had a motive for doing a less than adequate job treating her patient.

Continuing the investigation in New York City, Egan's wife is questioned by Frank and Tim. Just a few hours later, Egan's wife is killed and Egan's son is seen running. Kendall is taken into proctective custody until he gives up the suspect's name. Lennie Briscoe and Rey Curtis (From Law and Order) come to Baltimore. Munch finds out that Lennie knew his ex-wife a little too much (She moved to NYC after divorcing him). The suspect tried to escape in a seaplane but is caught. NYC ADA Claire Kincaid comes down to extradite him back to NYC, which made Frank upset. While extraditing him, the suspect has a heart attack and dies at the train station. (Part 1: "Charm City" aired on Law & Order: season 06, episode 13.)

Russert and Munch are assigned to work a case together; they find a retired cop who was murdered near his wife's tombstone. The dead cop's son asks Lewis, whom he went to the academy with, to get involved with case. He also makes his own inquiries, which get him into a bit of trouble. A suspect is arrested; however, despite the overwhelming evidence against the accused, the jury acquits him. The son contemplates delivering his own justice.

Jake Rodzinski has trouble dealing with the verdict of the trial and takes justice into his own hands. Kellerman is back from a family wedding in Wisconsin picks up the case of the murder of Kenny Damon. Lewis is not allowed to know all the details of Kellerman's investigation, because of his past relationship with Rodzinski, their chief suspect. Bayliss is at odds with Pembleton over the disposition of a grilled cheese sandwich.

The entire squad is put on 24-hour surveillance when a mass murderer has been identified, isn't at home and doesn't know that they know. Gee debates leaving the squad in the midst of the stakeout, so he can attend his daughter's wedding in California. As the detectives rotate through shifts on the stakeout, the main topics of discussion are the homeowners and Bayliss' plans to leave the unit.

A young girl is murdered, in a style similar to Adena Watson's murder. Frank demands to work the case alone as Bayliss begins to think that the two crimes might be related. Bayliss' obsession with trying to get this case solved and linked to Adena's murder causes the two of them to clash. Howard learns that Brodie has a crush on her and tells him she doesn't like the joke that's being pulled-- only problem there is that it's the truth.

Kellerman and Lewis (with Brodie) investigate a shooting at the New Moon motel, where everyone there has a motive for the crime. They split up and canvass the denizens of the motel; Lewis also searches for the victim's missing boot. The murder is just one of the many crimes that has occurred or is occurring at this establishment.

Lewis and Kellerman's investigation of a murder in a housing project puts them at odds with a civilian-patrol group, run by the Black Muslims. Munch is excited because Stan is scheduled to come back June 1st. Russert and Munch catch a case where both the victim and shooter are dead. She with Howard must decide whether to circumvent the so-called ""blue wall of silence"" among police officers when it is discovered that the officer on the scene didn't react in time. Barnfather stops Lewis and Kellerman's charging of a Muslim, until something is leaked to the newspapers. The ""big man"" is scheduled to come to the bar, but changes his mind, twice.

A prominent attorney is murdered and the murderer presents himself to Pembleton and Bayliss with a videotape that implicates him. Brodie works on increasing his self-image. Kellerman is determined to find out who's the ""lunch bandit."" The NSA steps in on Pembleton's murder investigation and provides him with a guilty party, even though they know he didn't do it. Bayliss' disgust with the interference doesn't sit well with Gaffney who wants to charge him with insubordination.

Lewis and Kellerman investigate a series of homicides that put them into the middle of a drug war. Kellerman suspects that Lewis is seeing someone, but he doesn't ""kiss and tell."" As the red piles up on the board Gee gets edgy. Kellerman seeks comfort from the godmother of the daughter of the victim's family. Kellerman and ""Drak"" have a confrontation. At a ""Peace on our Street"" demonstration, the current drug war is ended.

A trash-talking radio talk-show host makes a proposal to his listening audience. Lewis announces to Kellerman that he is getting married today, then he throws up. He motivates the rest of the squad to help him with the final details as he is getting married ""tonight after the shift ends."" Kay brings her sister with her to the station. Since the whole squad is busy with Lewis' wedding, Gee takes Howard out to work the homicide of the radio talk-show host. One of his listeners took him up on his proposal. Munch is skeptical about the Lewis wedding; he thinks it's an elaborate practical joke. Bayliss and Kellerman vie for the attention of Kay's sister. Gee shoots and kills a potential suspect, but the suspect was in jail at the time of the talk show host's murder. The guy who fingered him admits that he did it as a joke. The wedding is no hoax. During the festivities Pembleton's wife goes into labor.

Mary gave birth to a girl named Olivia; Tim is more excited about it than Frank. Their latest case involves a multiple shooting a restaurant. Lewis is back from his honeymoon, but while working a case with Kellerman, he confesses that they have yet to consummate their marriage. Later he tells him that they've separated. Tim stops by to see Frank and Mary's baby. They get a suspect for their case in the box. Frank collapses in the box while interrogating a suspect. Frank is put under the knife to release the pressure built up in his head from the stroke he had. After the surgery the doctor tells them that he doesn't know if Frank will recover.