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.

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.

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 shoot-out ultimately ensues.

Jane and Maura still aren't on speaking terms but are forced to work together when a college student, 25 year-old Rachel Lawson, is found strangled in the university's underground tunnels. She had also been renting a car every weekend for the last 20 weeks and was aware that her parents has separated. She had also spent a good deal of money on yoga in recent months. The yoga master, Sensei Matta, has recently bought 20,000 acres in Western Massachusetts and has a secret - one that lead to the death of Rachel Lawson. Meanwhile, Jane is surprised when her father knocks on her door. He has big news: he's going to be remarried - to a 28 year-old - but wants a church wedding so needs to have his marriage to Angela annulled. Tommy, who introduced his Dad to the woman, is having his own particular problems with the nuptials.

A musician is stabbed in a bar and the squad realizes that the stabbing victim had something to hide. Jane's father returns with shocking news.