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.

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.

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.

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.

More drug-related homicides are occurring. Pembleton is still relegated to desk duty and now so is Kellerman. A federal grand jury investigation is being conducted that goes back to the time when Mike was in the arson unit. Frank is still not taking his medicine and getting ready for the range test. Brodie moves out of Munch's place and into Bayliss'. Lewis finds out that the witness to his drug homicide has been brought downtown. He goes after him and meets Stivers, a female detective in narcotics. Lewis's witness points toward Luther Mahoney as the initiator of the contract. They go to find the executor, who's been executed. Stivers pages Mahoney and he comes in for questioning, but they can't make a case that Danvers thinks will stick. Frank misses a passing grade on his test by four points.

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

A four-year-old boy is abducted while riding a merry-go-round in the park under the supervision of his mother. The Homicide unit, which helps in the investigation of all child abductions, is called in and Falsone is the primary. When the boy's father has an alibi that checks out, the detectives beginning to check on known pedophiles and later they receive a call from the possible kidnapper. When that doesn't pan out, they start over. The host of a nationwide television program, This Weeks Wanted, suggests that they hypnotize the little girl who was riding on the horse next to the boy. Hypnosis reveals a partial plate number and that leads to a lucky break. Ballard and Stivers discuss motherhood and Falsone checks on his son.

Mike Kellerman's new vocation is private investigation, where the majority of the work involves catching cheating spouses. Falsone and Stivers catch a case where a newborn baby's body is found buried behind a motel. A young couple had checked into the room where the baby was delivered. The room was paid for using the girl's credit card. When they locate the girl (Debbie at home with her parents), she collapses and is brought to the hospital. The boy, Craig, is also located. Both say that the baby was stillborn; however, the autopsy reveals that the baby took a breath after it was born, so the death is ruled a homicide. Falsone notes that of the two, only the boy Craig seems to show any compassion for the baby. Kellerman meets Sheppard for a beer and tries to ask her about Falsone's baby case, later he asks around the squad room. Kellerman is hired to conduct his own investigation by the girl's defense team. Gee demands that Falsone and Stivers find convicting evidence before Kellerman