Jane and Maura's friendship suffers following the shooting of Maura's biological father, gangster Paddy Doyle. Jane also finds herself in the middle of an Internal Affairs investigation. And her relationship with Agent Dean is exposed.

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.

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.

Jane looks for a way for Maura to meet her biological mother, Dr. Hope Martin. Angela gets involved in a political campaign. And a nun from Jane and Frankie Jr.'s past returns.

Jane and Maura go undercover at a sex party to track down the perpetrator of a sex related murder in a mansion that's on the market. As Maura and Hope get better acquainted their relationship turns out to be especially important for Hope's daughter Cailin. Meanwhile, Sister Winifred tries to maintain some level of civility in the squad room.

The investigation of the murder of two doctors is hindered by a judge that won't sign a search warrant for his own personal reasons. Jane has to deal with a delusional secret admirer.

The gruesome murder of a bride and the disappearance of her sister lead Jane to a crazy jealous rival and a bigger even more gruesome criminal enterprise. Meanwhile Jane's brother and partner are dating Jane's next door neighbor which conflicts with Jane's moving plans but Jane is more concerned about her neighbor's profession.

Jane investigates the death of a family friend in a boy band with a history of drug abuse. It looks like a drug case until drug tests come back negative and another rocker turns up dead. Maura's soft heart drags Jane into assisting with Lydia's pregnancy despite her disapproval of her mother's relationship with Lydia.

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.

The murdered man is in AA with Vince's ex-wife-he is not her husband. He lost his high-paying job in a pharmaceutical company and now is just a lowly pharmaceutical rep with a conscience, a past, and a plan for redemption.

A famous author who apparently hanged himself, a charitable gift for helping put a man on death row, a nagging feeling, a health program for the squad room, a suicide chat room, an evasive witness, a mother who insists her son is innocent, and a man who fell from a roof make for another week of mysteries and distractions in Jane's and Maura's investigations.

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.

Casey drops some big news to finally explain to Jane why he's keeping his distance. Barry's mother plays ringer in an interoffice softball game then announces she's getting married. The detectives investigate the murder of a an ex-football player who ran a bakery.

Hope is ready to talk to Maura about a kidney for Cailin. Jane pays an unannounced visit on Casey. A substandard building related to a murder investigation endangers Jane's friends.