Jane deals with emotional and physical scars as old loves re-appear and her mother Angela deals with divorce. Meanwhile Jane's ex-con brother Tommy has eyes for cerebral Maura, whose own family life is complicated by her adoptive mother Constance and a biological dad with a link to the Mob.
After taking a bullet in the Season Finale during a siege of the precinct, Jane Rizzoli is honored as a hero at a public event. The celebration is short-lived, however, when disaster strikes. The ensuing case reunites Jane with an old high-school flame, Sgt. Major Casey Jones, who may be just the person she needs to heal her emotional scars.
Jane and Maura's relaxing day at an outdoor spa is anything but when they discover the murder of a pregnant woman serving as a surrogate mother. Soon the hunt is on to find the baby's biological parents.
Shortly after sailors invade the streets of Boston for Fleet Week, a young girl is found dead. Frost's father, a Navy Admiral, comes to town, causing tension with his son. And, Maura goes on a date with Angela's mechanic.
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.
Jane and Maura investigate after the coach of the Boston Pilgrims baseball team is found dead in the locker room. The death comes as a star player and the team owners battle for control of the team. Meanwhile, Jane's brother Tommy returns home after being released from jail.
A Revolutionary War re-enactment becomes the scene of a real killing when a soldier turns up dead. Maura's extensive knowledge of American history becomes important as she and Jane try to solve the case. And Maura's brilliant mother, Constance Isles, comes to Boston for an art exhibit.
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.
When a young dockworker is found dead, the team discovers that there are mob connections; Jane tries to avoid sensitivity training; Maura starts spending time with Jane's brother.
The shooting of a community activist brings out a witness who's willing to testify. TV host Bill O'Reilly airs his disapproval of the police department.
Boston Homicide teams up with the FBI after a bank manager is shot during a robbery. Jane’s brother Tommy may be facing more trouble just as his relationship with Maura begins to grow. Tessa Thompson guest-stars as by-the-book FBI Agent Anna Farrell, who has a complicated history with Detective Frost.
Jane attends her high school reunion and brings Maura along for the ride, but the fun is cut short when one of her old classmates turns up dead on the football field. Jane must focus on the past when she realizes everyone in her class is a potential suspect. Meanwhile, Korsak gets a visit from ex-wife Melody Patterson (guest star Lolita Davidovich), who hopes he’ll invest in her new business. Chris Vance returns as Sgt. Major Charles “Casey” Jones, an old flame of Jane’s, and Matthew Del Negro guest-stars as Angela’s car mechanic, Giovanni, who once had eyes for Maura.
The world of competitive dance turns deadly when the mother of a star performer is stabbed to death at a competition. Jane and the team search for clues, but they soon realize something is off about the woman’s history. Korsak has his hands full when his stepson is accused of shooting a cop. Guest star Lolita Davidovich returns as Korsak’s ex-wife Melody.
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. Guest star Billy Burke returns as FBI Agent Gabriel Dean, who hopes to rekindle his relationship with Jane. And guest star Jacqueline Bissett reprises her role as Maura’s mother, Constance Isles.