An unknown man is killed with an ice pick pierced into his ear. Police find that he is Colin Doyle, son of the Irish mob enforcer, Patrick Doyle, the actual target of gang rivals. Dr. Isles is in an emotional upheaval about the dead man.

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.

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.

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.

Jane and Maura investigate the death of a young woman who is found washed up on the beach. Maura confirms that she drowned and manages to trace the exact location by analyzing the water in her lungs: a tank in an old fish factory. Jane is somewhat upset to find that an old flame, police Lt. Rafael Martinez, is back in Boston. They had worked together in the narcotics division but their relationship ended after a confidential informant had been killed and Martinez left to join a special task force some 8 years ago. The dead girl is identified as Brenda Thompson, a journalism student who was pursuing a drug story on her college campus. When Jane finds Lt. Martinez's business card among her possessions, it seems that he was using her to get information. Meanwhile, Maura learns that she may be in danger owing to her father's activities.

The decades-old death of a mother and child open a closet door revealing skeletons that threaten to complicate the start of Paddy Doyle's RICO trial.

The murder of a rare bookseller brings Jane and Maura into the world of Keltic writings and coded confessions, just as Maura is preparing Jane to meet her new man. Angela's relationship with Cavanaugh changes pace.