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 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.

Rizzoli gets a bravery medal after escaping from a hostage situation. A brave US military private is also felicitated but is killed by a car bomb after the ceremony. Rizzoli, resting for the last three months and yet unfit, investigates.

The Boston Pilgrims baseball team is co-owned by a man and his estranged wife. Rizzoli and Dr. Isles probe the mysterious deaths of the team's coach and a star player. Tom Rizzoli, a home burglar now out on probation, is misunderstood.

Jane Rizzoli and Maura Isles find themselves investigating a death that occurred during the re-enactment of of a Revolutionary War battle organized by a university professor, Dwayne Cravitz. They soon determine that far from being an accident, the shooting was from a sniper who was actually out to kill Cravitz. A DNA sample leads them to believe that the shooter is someone from his past. Maura meanwhile is thrown for a loop when her mother, the rich and beautiful Constance Isles, drops in for an unexpected visit. They have a strained relationship however with Mrs. Isles not quite sure how to be a mother to her daughter and Maura feeling intimidated and reduced to babbling in her presence.

Jailed Hoyt is dying of cancer and Randall, his fellow inmate, is murdered. Hoyt conveys confusing images to Rizzoli who then attempts to connect deaths of Randall and of the four Wilsons in 2005, to Hoyt. Rizzoli's birthday is celebrated.

After the murder of much-loved community leader Elmore Gregory, Dante Morgan steps forward to identify the shooter as a gang leader, Terence Jones, also known as Little T. On the night before the trial, Dante leaves his police protected hotel room and is found dead the next day in a gang-ridden neighborhood with "snitch" written on his forehead. With the main witness out of the way, the only other evidence against Jones was obtained using information from one of Vince Korsak's confidential informants. When Vince says he can't produce him for the court, the judge gives the prosecution 48 hours of the case will be dismissed. Meanwhile, TV's Bill O'Reilly is in Boston to cover Little T's trial. Jane's mother Angela is a big fan and at a book signing she gives him Jane's cellphone number.

Jane and Maura investigate the stabbing death of Denise Ryan, who stumbled onto the stage at her daughter Dakota's dance competition with a pair of scissors in her chest. According to the dance studio owner, Coach JJ, Denise wasn't like the other moms and didn't get to know her very well even though Dakota has been going there for two years. The husband is eliminated as a suspect but the police responded to a disturbance at the dance studio two weeks ago when two of the other moms, Yvonne and Kim, got into an argument. When they learn that Denise had no credit history whatsoever, they realize that the plastic surgery she underwent was likely to hide her true identity. Korsak meanwhile has been avoiding his ex-wife Melody who wants him to co-sign a lease so she can open her yoga studio. He learns that his stepson Josh has been arrested for shooting a policeman with his own gun. Joss is angry and refuses to speak to anyone.

When a warehouse fire kills a firefighter, Jane and Maura must investigate whether it was arson or an accident. But the investigation hits a snag when a hit-and-run leaves someone in the hospital.

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.

In the season premiere, a community parade turns deadly and family tensions and politics arise. A surprise visit from Lt. Col. Casey Jones (CHRIS VANCE) reveals shocking news.

Jane and Maura investigate the death of a young woman who is found washed up on the beach. Maura confirms that she drowned and manages to trace the exact location by analyzing the water in her lungs: a tank in an old fish factory. Jane is somewhat upset to find that an old flame, police Lt. Rafael Martinez, is back in Boston. They had worked together in the narcotics division but their relationship ended after a confidential informant had been killed and Martinez left to join a special task force some 8 years ago. The dead girl is identified as Brenda Thompson, a journalism student who was pursuing a drug story on her college campus. When Jane finds Lt. Martinez's business card among her possessions, it seems that he was using her to get information. Meanwhile, Maura learns that she may be in danger owing to her father's activities.

Dr. Isles becomes the suspect in the murder of a mysterious guest of a charitable fund-raiser.

The decades-old death of a mother and child open a closet door revealing skeletons that threaten to complicate the start of Paddy Doyle's RICO trial.

A reclusive hoarder becomes the subject of an investigation into the murder of a city sanitation employee.

The hit-and-run murder of a high school science and driver's education teacher focuses on a group of friends who were also students of the victim.

"Sports rage" and angry hockey parents are the focus of the investigation of the murder at a youth hockey game.

When someone begins to stage copycat murders presented at a symposium on serial killers, detectives believe the suspect is one of the meeting participants.

The squad gets involved in an incredibly dangerous scenario when a horrifying incident occurs during a drag race; Jane gets a lead that points to drug trafficking being the motivation for a murder; an investigation is hindered.

A mock trial advisor (A'DA ALISON WOOLFOLK) dies during a competition. Meanwhile, Jane is concerned that Angela may be hiding financial issues. DOUG SAVANT also guest stars.

Two puzzling murders share a surprising link that could be the key to finding the perpetrators. Meanwhile, Jane and Casey come to a crossroad and Maura assumes caretaker for Patrick Doyle, Sr. who is being released from prison.

The Boston Police department is haunted from the past when a man in clown-costume almost kidnaps a little boy. Is it the same person that has molested and kidnapped boys in the 1980s?

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.

When a food truck chef dies suddenly, all signs point to a suspicious poisoning, but many questions remain unanswered. Meanwhile, Tommy announces some big plans that have Angela very excited. And Maura's birth mother, Hope, takes a bold step toward making amends with her daughter.

Homeland Security steps in when a senator's daughter is found murdered. The squad rushes to solve the case, which could put national security at risk. Meanwhile, Tommy and Frankie get into a fight after Tommy starts slipping back into bad old habits. And Jane reveals some shocking news that could change her life forever.

As the Boston Homicide detectives solve a murder, they each think of ways to say goodbye to Detective Barry Frost.

The murder of a rare bookseller brings Jane and Maura into the world of Keltic writings and coded confessions, just as Maura is preparing Jane to meet her new man. Angela's relationship with Cavanaugh changes pace.

The decades-old death of a mother and child open a closet door revealing skeletons that threaten to complicate the start of Paddy Doyle's RICO trial.

In the season premiere, a community parade turns deadly and family tensions and politics arise. A surprise visit from Lt. Col. Casey Jones (CHRIS VANCE) reveals shocking news.

A reclusive hoarder becomes the subject of an investigation into the murder of a city sanitation employee.