A serial killer named the Surgeon once tried to kill Boston Detective Jane Rizzoli. Still serving time, his 'signature' killings recur. Rizzoli, together with Medical Examiner Dr. Isles, pursue them, while the Surgeon escapes from prison.
Rizzoli pursues strangling deaths, suspense-fully reminiscent of the now long dead Boston Strangler, who a retired cop believes to be alive. Her new Boss, a childhood tease, is unbelieving. Clinically inclined Dr. Isles ruins a date.
Jane and Maura investigate the mysterious death of a young boy whose family is from Cape Verde. It appears at first that he may have died during an attempted exorcism, and it may take a message from beyond the grave for Jane to pinpoint exactly what happened. Jane is distracted from the case when her mother sets her up on a surprise date.
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.
Jane and Maura investigate the murder of a young woman who was found beaten, raped and strangled outside a gay bar. At the scene they find a flyer from an anti-gay organization and their first thought is that they are dealing with a hate crime. The victim was married and her same-sex spouse says everything was fine between them, though the fact that she was out at a bar alone suggests she may have been cheating. The victim had a resemblance to Jane who goes undercover at the bar, with Maura working there as a waitress to collect fingerprint samples from anyone Jane ...
Rizzoli and Dr. Isles run the Boston 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.
The actions of Hyot, alias the Surgeon, and Rizzoli's nemesis, from inside solitary confinement spook her. While Rizzoli is off the Hoyt case, Dr. Isles does facial analysis of Hoyt for clues on murder/ disappearance of a married couple.
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.
An under-cover cop is killed by a drug ring. They then attack police HQ to retrieve a crucial piece of evidence found by Rizzoli at the crime scene. Rizzoli, Dr. Isles and others are trapped inside the HQ. A tense shoot-out finally ensues.