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 works a strangulation murder after a body is dumped at the PD softball game.

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.

A college student is shot dead on campus. Meanwhile, Jane's mother Angela gets into a spat with her father over her car.

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 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.

Still suffering from nightmares of Hoyt, Jane finds a "gift" left outside her home. While she deals with that, the team investigate a missing person found murdered and posed on a park bench.

A young man is found murdered, stabbed to death with an ice pick, which was left sticking out of his ear. An MO that reminds Korsak of old school mob hits.

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.