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 might meet. Meanwhile, Jane goes with someone from her yoga class - Maura encourages her he doesn't quite meet expectations.

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.

The actions of Hoyt, 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 shoot-out ultimately ensues.