Rizzoli gets a bravery medal after escaping from a hostage situation. A brave US military private is also felicitated but is killed by a car bomb after the ceremony. Rizzoli, resting for the last three months and yet unfit, investigates.

A pregnant woman is stabbed to death but Dr. Isles saves her baby. The husband is suspected. Police find that the baby is surrogate and has also been sold online in adoption. During kangaroo volunteering, a suspicious nurse is observed .

From among thousands of sailors in Boston during Fleet Week, an unknown sailor is suspected of two rapes and murders. Admiral Frost appears and he and his son Detective Frost do not see eye to eye. Policeman Rizzoli Jr. plays a part.

When the daughter of a police officer is kidnapped in front of her younger brother, Jane and the team race to find the girl, fearing her abduction is connected to another case in which a young girl turned up dead only hours earlier.

The Boston Pilgrims baseball team is co-owned by a man and his estranged wife. Rizzoli and Dr. Isles probe the mysterious deaths of the team's coach and a star player. Tom Rizzoli, a home burglar now out on probation, is misunderstood.

Jane Rizzoli and Maura Isles find themselves investigating a death that occurred during the re-enactment of of a Revolutionary War battle organized by a university professor, Dwayne Cravitz. They soon determine that far from being an accident, the shooting was from a sniper who was actually out to kill Cravitz. A DNA sample leads them to believe that the shooter is someone from his past. Maura meanwhile is thrown for a loop when her mother, the rich and beautiful Constance Isles, drops in for an unexpected visit. They have a strained relationship however with Mrs. Isles not quite sure how to be a mother to her daughter and Maura feeling intimidated and reduced to babbling in her presence.

Jane and the team investigate what appears to be a modern-day witch hunt in Salem. Meanwhile, Frankie's old girlfriend returns to town with a surprise, and Jane has no problem speaking her mind about the situation.

Evan Dunbar and son Chris, customs brokers, are attacked, killing Evan and injuring Chris. Chris' subsequent actions and Evan's brother, just released, are suspected. Isles' old flame Dr. Faulkner visits and Rizzoli's mom is suspicious.

22 year old Melissa finds her dock-working father's work place injury fishy. Her subsequent murder has the mob's M.O. But, an injured Doyle, the mobster and Isles' father, claims innocence. Rizzoli frowns on Isles' chess game with Tom.

Jailed Hoyt is dying of cancer and Randall, his fellow inmate, is murdered. Hoyt conveys confusing images to Rizzoli who then attempts to connect deaths of Randall and of the four Wilsons in 2005, to Hoyt. Rizzoli's birthday is celebrated.

After the murder of much-loved community leader Elmore Gregory, Dante Morgan steps forward to identify the shooter as a gang leader, Terence Jones, also known as Little T. On the night before the trial, Dante leaves his police protected hotel room and is found dead the next day in a gang-ridden neighborhood with "snitch" written on his forehead. With the main witness out of the way, the only other evidence against Jones was obtained using information from one of Vince Korsak's confidential informants. When Vince says he can't produce him for the court, the judge gives the prosecution 48 hours of the case will be dismissed. Meanwhile, TV's Bill O'Reilly is in Boston to cover Little T's trial. Jane's mother Angela is a big fan and at a book signing she gives him Jane's cellphone number.

Jane's younger brother Tommy seems to be settling down. He's getting work here and there and is moving into his own apartment. He still sees Maura from time to time but she would like to keep their relationship a platonic one. Meanwhile, the homicide squad investigates a bank robbery where the manager was shot by one of robbers for no apparent reason. They immediately cross swords with the FBI who also have jurisdiction and Det. Barry Frost in particular seems to have it in for the Special Agent in charge, Anna Farrell. This is the second robbery committed by these men and they soon find the getaway vehicle with one of the robbers inside, shot to death. It all becomes very personal for Jane when her brother Tommy's fingerprints are also found in the vehicle.

After her boyfriend Casey Jones is unable to get to Boston, Jane takes Maura to her dreaded high school reunion. She hates most of the people there but one former classmate that she liked, Steve Sanner, says he would like to discuss something with her. Before he can do so however, Steve is shot and killed while taking a walk on the football field. The killer used a steel wool-filled water bottle as a silencer. He worked for another high school classmate, Rory Graham, who says he wasn't having any trouble at the office or with co-workers. Based on his phone records, they suspect he may have been having an affair with another former classmate, Debbie Tibbet, but when she is found dead her husband tells the police she had recently become very secretive. A third dead classmate gives them the clue they need to identify the killer. Meanwhile Vince Korsak's ex-wife is back in town wanting money for a new enterprise. Vince would like to see his 16 year-old son Josh.

Jane and Maura investigate the stabbing death of Denise Ryan, who stumbled onto the stage at her daughter Dakota's dance competition with a pair of scissors in her chest. According to the dance studio owner, Coach JJ, Denise wasn't like the other moms and didn't get to know her very well even though Dakota has been going there for two years. The husband is eliminated as a suspect but the police responded to a disturbance at the dance studio two weeks ago when two of the other moms, Yvonne and Kim, got into an argument. When they learn that Denise had no credit history whatsoever, they realize that the plastic surgery she underwent was likely to hide her true identity. Korsak meanwhile has been avoiding his ex-wife Melody who wants him to co-sign a lease so she can open her yoga studio. He learns that his stepson Josh has been arrested for shooting a policeman with his own gun. Joss is angry and refuses to speak to anyone.

When a warehouse fire kills a firefighter, Jane and Maura must investigate whether it was arson or an accident. But the investigation hits a snag when a hit-and-run leaves someone in the hospital.