When the winner of the city's Good Samaritan Award is murdered, Gee and his staff are called to help the new female night shift commander. Pembleton is at odds with the detective he shares a desk with. Beau and his wife separate and Kay gets caught in the middle. Meldrick and Munch have plans to buy a bar and try to persuade Bolander to also become a partner. Bayliss agrees to become a ""silent"" partner. In passing, Crosetti is said to be in Atlantic City on a ""shots, slots and sluts"" dream vacation.

Gaffney allows a possible murder site to be washed down which causes Pembleton to go off on him. Russert takes Gaffney off the case and Pembleton is made the primary. Things get more complicated as a second victim is found. Beau tries to decide between his family and his relationship with Megan and he confides in Kay; his wife tries to reconcile with him. Russert wrestles with the media demands about the case. Something from Bayliss' past comes out when they try to get the liquor license for their bar. Bayliss goes to the liquor commissioner to work things out. A collector of the macabre comes in search of the victim's white gloves. A third victim is discovered.

The church asks that the public know the details of the murders. Pembleton has an interesting time in the box with a witness who has multiple personalities and is shown to be the killer, but before he can get a confession, her lawyer arrives and later she confesses on television. Pembleton begins to question his faith. Bayliss becomes a not-so-silent partner. Beau spends some time with his family and decides to end his relationship with Megan.

A young man comes into the squad room and after getting their attention, tells the detectives that his brother has been shot. Pembleton is sued by the multiple personality serial killer, who states he violated her civil rights during interrogation; he is discouraged when the city agrees to settle out of court. Munch must attend an alcohol awareness seminar to meet a requirement for the bar. Lewis has ""love at first sight"" with a woman who makes models of crime scenes, but she has ""love at first sight"" when she sees Bayliss and he sees her. Later, they attend an art exhibition and have an unusual sexual encounter in her ""bed."" All is not well at the Felton household, when he returns home to a cleaned out house.

Bayliss continues his relationship with the artist, but she's told her boyfriend. When she tells Bayliss that her boyfriend hit her upon hearing the news, it makes Bayliss so mad he confronts him. Pembleton and Bayliss investigate the death of a woman who's received a delivery of fresh flowers, although she's been dead over two weeks. Bolander and Munch investigate the shooting of Thorne's source, who's linked to a cocaine cartel, then Thorne is shot. Gee tries to get the department to get him a replacement for Crosetti. Thorne's daughter decides to keep his newspaper going. Beau tries to find out where his wife has moved the family. With Meldrick and Bayliss' disagreement over the artist, Munch is left without partners for the bar. Bayliss goes over the edge when the artist dumps him, so he holds up a liquor store for 11 cents; Pembleton gets him out of it.

Crosetti's body is found and Bolander is the primary and he thinks the evidence points to suicide. If it is a suicide, there will be no honor guard for the funeral. Refusing to accept the death as a suicide, Meldrick launches his own investigation and tries to thwart Bolander's investigation. Bayliss and Pembleton make arrangements for the funeral reception. Pembleton has reservations about going into the church for the services. Munch works with his brother, an undertaker, to arrange for a coffin. The preliminary ME report shows Crosetti had a blood alcohol level of .25 and wide variety of anti-depressants, The verdict: suicide.

After uncovering the fact that an elderly woman's tongue was cut out, Kay decides it is time to take a vacation. She returns home and while she is there she looks into the murder of an environmentalist. The suspects include her brother, an ex-beau and their co-worker. Pembleton reluctantly becomes Felton's partner and they finish investigating the murder of the elderly woman. Munch is against having a television put in their bar.

Munch spreads his usual Christmas cheer. Russert, who misses detective work, joins Meldrick on an investigation into the murder of a material witness, when she discovers she knows something about the victim's case. Munch and Bolander investigate the death of a man in a Santa Claus suit and Munch spends the evening with whom they believe is the victim's son. Beau buys Christmas presents for the kids, although he still doesn't know where Beth and the kids are. Bayliss searches the station in search of a game of hearts.

Pembleton and Bayliss investigate the shooting of a young boy. During the investigation, the mother of the victim meets the mother of the shooter in the aquarium. The shooter shows no remorse for the killing, although he shot the wrong kid. Munch, Bayliss and Lewis can't remodel the bar when they discover it's been classified a historical landmark. Then when they find out back taxes are due on the building, which shuts them down before they open. Beau finds out his kids are in Upper Darby, Pennsylvania, so he goes to find them.

The deputy commissioner invites Pembleton to lunch and gets him to investigate a case involving a congressman. Beau hires a private detective to find Beth and the kids when his clue that they are in Wilmington falls through. Howard and Felton investigate a case of a dead homeless man. Their job is made more difficult when they can't find the body. Lewis and Munch investigate the death of a motorcycle gang member. Pembleton finds out the truth, participates in the cover-up and then resigns when the media gets hold of the real story and the deputy commissioner doesn't back him up.

Russert's old partner joins the homicide unit, but she suspects that he is taking his work frustrations out on his wife. Pembleton struggles with his pride and domestic life as Gee and Bayliss try to convince him to return. Bayliss is partnered with Lewis and on the way to the crime scene gets the ride of his life. Bayliss tangles with a reporter. Beau is in Philadelphia with his kids. The bar has its grand opening.

Bolander, Munch, Howard and Felton all meet to serve a warrant, but Bolander, Howard and Felton are shot in an ambush. Pembleton becomes the primary in the investigation and is partnered with a detective who specializes in the psychology of their prime suspect: a pedophile. Stan's ex-partner Mitch Drummond offers his help. Kay's father and Beau's wife and the kids come to the hospital. A clerical error is discovered to be the cause of why the detectives went to the door marked 201, instead of 210.

The detectives continue chasing their only lead, the child molester. Munch is teamed with Stan's old partner. Beau has no feeling in his foot, but feels guilt about Kay's condition. Stan's ex-wife arrives in town, but has a hard time going to see him at the hospital. Barnfather and Granger want Russert to review Gee and see if he was negligent in his duties regarding the paperwork that led to the shooting. The pedophile is located and it is discovered he was responsible for the strangulation of a young boy, but not the shooting of the three detectives.

Bolander has a relapse. The detectives sound off to the local news about the shooting. Apartment 201 is opened up and the occupant, Gordon Pratt, is a gun freak who once tried to be a cop. Russert and Howard declare a truce. They find the shooter, but lack of a weapon gets him released; later he is found with a bullet in his head.

Pembleton receives an extradited prisoner from New York City Detective Logan. Bayliss is put in charge of investigating the death of Gordon Pratt, but gets no cooperation from anyone on the force. Beau wants to return to active duty. A woman recognizes Munch from an old picture that is hanging in an art gallery across from the precinct. To Munch's embarassment he discovers that an old girlfriend, who's a photographer, is displaying an old picture of him in the buff at her gallery showing. Pembleton and Meldrick investigate a random shooting of a woman, and they clash over where the weapon may have been fired. They also find a woman who's shot her boyfriend and stuffed him in the freezer. Beau accompanies Gee on an investigation and must come to grips with his inability to look at a dead body the same way.

Beau meets Megan's cousin, NBC's Tim Russert. Kay and Stan return to duty, after Stan undergoes a final test, and Kay finds her desk has been moved. They, like Beau, must both get used to the job again. Tim and Beau investigate the discovery of a skeleton found buried in a backyard. Bolander and Munch discover an unlikely suspect in the murder of a quiet elderly couple: their grandson. Gee exposes Granger, who used his relatives in some department plumbing contracts; the information is leaked to the papers, Granger is forced to retire. Barnfather is made colonel and a new captain is named, Megan Russert. The higher ranks of the Baltimore police department are now more politically correct, but Gee doesn't like it.

A 16-year-old murder case must be reopened when the daughter of the convicted killer holds Col. Barnfather hostage. Pembleton and Bayliss investigate an elderly man whose wife died of drowning in the bathtub. Gee and the newly appointed Capt. Russert clash over the handling of the hostage situation. Bolander, Munch, Howard and Felton must go to the archives to find the records of the case. Lewis meets a strange homeless man who's witnessed the suicide of a man who committed the original murder and the detectives race to overturn the previous conviction. A new ""old"" bartender tries to convince Munch to go with the latest rage, microbreweries. Bolander and Lewis try to connect the suicide victim to the man on death row.

Crosetti's caseload is distributed among the detectives and Howard's 100% clearance rate may be in jeopardy when she gets his most difficult unsolved case; this is further complicated when Beau misplaces some new evidence. Gee meets one of Megan's friends at lunch and is convinced she isn't interested in him because he is too black. The guys close on the bar but wind up penniless when they must pay extra fees that they weren't aware of. Beau looks to Megan for comfort when he can't recover the evidence and it looks as though Beth and kids are never coming back.

Tim's cousin shoots a Turkish exchange student and his partnership with Pembleton may be in jeopardy when they both stand on opposite sides of the case. Lewis hires his grandmother to cook at the bar.

A convict is released from prison and begins to get his revenge on Frank by frustrating the investigation he is currently working on and also by terrorizing his wife.

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 protective custody until he gives up the suspect's name. Lennie Briscoe and Rey Curtis come to Baltimore. The suspect tried to escape in a seaplane but is caught. This crossover started on Law and Order S06E13 Charm City (I).

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.