After a student is gunned down in broad daylight, the investigation reveals she had more than a few secrets. Meanwhile, Jane's mother Angela gets into a spat with her father over the car.

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.

Evan Dunbar and son Chris, customs brokers, are attacked, killing Evan and injuring Chris. Chris' subsequent actions and Evan's brother, just released, are suspected. Isles' old flame Dr. Faulkner visits and Rizzoli's mom is suspicious.

Jane and Maura investigate the murder of an army veteran, 29 year-old Bernard Avery, who was killed in an alleyway with a hatchet. He was homeless, one of many ex-servicemen now living on the streets of Boston, and suffered from PTSD. When Rizzoli and Korsak visit a psychology center where Avery had sought help, Jane is surprised to find her old friend Casey Jones working there. He's been back for several months but refuses to tell her anything more. The police soon have a second dead homeless vet and Jane's informant, Rondo, thinks he's found a witness. Meanwhile, Maura meets Dennis Rochmond and after saving his life, he sends her orchids. She also discovers her wild side.

Young female professionals dressed as dolls are turning up dead on the public transit system, and Jane and Maura must piece together the clues. Angela implements new ideas for the café. And Jane learns more about how Casey was injured.

Frankie's promotion to detective goes to someone the detectives have a history with. The man Maura saved in the morgue returns to a cold reception. The case of the week is a body encased in plaster on public display on a fountain and it's not the first or the last.

A mentoring program, a fire alarm, Angela's missing wallet, and Angela's breakup with the lieutenant distract the detectives as they track the killer of a microbrewer through cyberspace.

Baby TJ's christening turns grim when a body is discovered in the church. Jane almost abuses her power in order to protect her brother Tommy (COLIN EGGLESFIELD).