Rizzoli and Dr. Isles look at the death of the head of the rich, Brahmin Fairfield family. Dr. Isles once dated the dead man's brother and Rizzoli feels that this is hampering work. Rizzoli's mother peddles juices with dubious benefits.

Rizzoli and Dr. Isles run the Massachusetts Marathon and find a dead runner at Mile 3 and Mile 12 marks. Impossible to get back-up, and fearing more deaths from panic and stampede, they silently endeavor to solve the crimes as the race continues.

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.

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.

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.

Jane and Maura's friendship suffers following the shooting of Maura's biological father, gangster Paddy Doyle. Jane also finds herself in the middle of an Internal Affairs investigation. And her relationship with Agent Dean is exposed.

Dr. Isles becomes the suspect in the murder of a mysterious guest of a charitable fund-raiser.