Bayliss and Pembleton continue to struggle with the Watson case. Bolander and Munch discuss ""iguana style"" and are called to check out the homicide of a victim that isn't dead, at least the first time they're called. While checking out some leads for the Watson case, Crosetti gives his theory on the conspiracy to kill Abraham Lincoln. Lewis wants to flood Memorial Stadium. Bolander expresses an interest in Dr. Blythe; Munch advises and sends flower's in Stan's name. Danvers needs a stronger case; however, Howard is frustrated with a dead end. Then the ghost of the victim leads her to the undiscovered proof. Tim attends Adena's funeral.

Crosetti and Lewis investigate the shooting of a fellow police officer whom Crosetti regards as a son, Howard suspects a rabid Spiro Agnew fan of murder but ends up solving the Calpurnia Church case meanwhile Bolander makes a friend whose death interrupts his date with Dr. Blythe.

Crosetti focuses his investigation into the shooting of Officer Thormann on one suspect, while Lewis continues to investigate. Meanwhile, Pembleton and Bayliss pursue different leads in the murder case of eleven-year-old Adena Watson.

Pembleton and Bayliss have only twelve hours to grill their prime suspect in the Adena Watson case before they must let him go.

While Giardello is busy sending off an old friend to retirement Pembleton and Bayliss investigate the murder of a dog, Howard and Felton argue over whether Felton finds Howard attractive while dealing with a drug-related homicide and Bolander and Munch take Dr. Blythe's son on a ride along. Meanwhile, Crosetti takes care of the bed-ridden and blind Thormann.

Howard and Felton are in court over the Pony Johnson case, Crosetti and Lewis go head to head with the Secret Service and Bolander and Munch argue over drug legalization. Meanwhile, Pembleton gets an unexpected job offer.

Quitting smoking dominates the conversation ad behavior of the homicide detectives even as they solve what may be a gang-related killing of a 14-year-old boy. Lt. Giardello discovers a secret asbestos removal project on the third floor and confronts his superiors on behalf of his squad.

The homicide team pulls the graveyard shift on the hottest night of the year. Bayliss is consumed by the Adena Watson case, driving a bigger wedge between him and partner Pembleton. Giardello finds a baby in a cage. A renegade Santa Claus runs loose in the building and the whole squad tries to figure out who's responsible for a candle that keeps getting lit.

All the detectives scramble to solve the case, when the mother, in a family on vacation, is murdered during a holdup. The husband has a hard time dealing with the reality of him not doing anything during the situation and Felton's indifference. When the suspects are found Howard is convinced that the youth who confesses to the murder didn't do it.

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.

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.

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.

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.

A riot breaks out at the prison, where two inmates are killed. The squad goes to the scene, but Frank must still stay behind. Bayliss, Lewis, Kellerman and Howard interview the inmates; many of them have familiar faces. Frank works on his target practice. Bayliss thinks that one inmate really wanted to tell him something, so he puts together a deal to get the information. The inmate confesses to the murder and Bayliss doesn't believe him. Another riot breaks out and the truth is finally discovered.

Brodie suggests that a classmate of his named Schack should be a suspect in the death of the student that Munch believes committed suicide. Frank and Mary meet with their marriage counselor and they begin to air some issues. Bayliss and Kellerman try to link together two deadly bombings. Schack attacks Brodie, but he can't prove it. He does offer a way to get Schack to admit to the murder. Frank tells Mary that he will agree to getting Olivia baptized. Mike connects the two bombings; the victims were both connected through the death of the Korean grocer who was murdered by a man who worked for Luther Mahoney. They suspect that there may be more bombs, including one at the courthouse where Meldrick and Julianna are waiting to meet with Judge Aandahl and Danvers, both of who were associated with the Korean grocer case. Frank arrives late to the baptism; Mary takes this as a sign and tells him she is leaving him for a while.

Mike and Julianna wake up the morning after a night of drinking and passion. The investigation into Beau's death continues; Howard wants to be the primary while Frank tries to maintain control. Gee asks her to step aside and let him do the job with a more unbiased approach. The investigation creates some unlikely pairings: Pembleton with Gharty and Bayliss with Falsone and Munch on his own. Meanwhile, Howard and Russert make arrangements for Beau's funeral. Lewis and Kellerman's investigation into a homicide is stalled; when Kellerman's hangover laden police work is shoddy. When it appears as thought the investigation is going nowhere; Kay demands to be put on the case. Gee refuses. Because of his bad day and finding Julianna drinking with someone at the Waterfront Bar, Kellerman suggests that they should stop drinking. Frank tries to call Mary; eventually they connect and reconcile; with Frank saying that he is willing to give it all up. They find out who killed Beau, but when they go

Bayliss returns to duty to discover the bosses have renovated the squad room in an attempt to make everyone forget the tragedy of last May. Gharty and Ballard have also returned and Ballard debates about whether she should ask Falsone to the Lodge party. New detective, Rene Sheppard, tells her just to go for it. Seizing the opportunity, Lewis goes for it and asks Sheppard to the party; it seems that he and Barbara have separated and are on their way to divorce. Meanwhile, Falsone speculates if he should ask Sheppard to the party. The first case Bayliss catches, now partnered with Munch, involves the dismembered body of Angelo Faltislo, a friend of Gee's cousin, Mario Giardello. Stivers and Falsone's case is similar: Leo Grimaldi, another friend of Mario, is also found dead. When Gee goes to question cousin Mario, he finds Mario's body in the same condition as that of his friends. Gee's estranged son, Mike Giardello, an FBI agent in Arizona, returns for the funeral. Mike asks Falsone (w

Sheppard and Bayliss await the trial of Luke Ryland, the Internet killer. A number of delays keep the hearing from being held; the last time it is because Danvers can't make it due to being held up in another trial. Because of a technicality in the law, Ryland is set free. Bayliss is outraged and winds up pushing Danvers, who later threatens to put Bayliss up on charges. Gee's daughter Teresa arrives, to help with the celebration of her father's promotion. Gee asks Bayliss to apologize to Danvers and Bayliss declines. Lewis and Falsone look into the murder of a drug addict whose husband looks like the most probable suspect. The victim's mother-in-law isn't very cooperative and her sister is a nun who thinks her brother-in-law is an architect. Gee worries about whether or not he will be able to perform in his new role as Captain of the property crimes division, later he turns down the promotion. Bayliss and Lewis have words about the way each other handle their memories of the past.