When Rizzoli and Maura investigate a murder of a wealthy couple, they find out that the serial killer is known as "The Surgeon", the one who almost killed Jane. With "The Surgeon" in prison, it is clearly his Protege that has picked up from where it ended. Guest star: Billy Burke.
A possible copycat to the Boston Strangler is lose and Rizzoli and her new boss don't see eye to eye. Meanwhile, Maura gets reprimanded for diagnosing everyone around her.
When Rizzoli and Maura investigate a murder in Cape Verde of a young boy, all signs point to him dying during a botched exorcism. Rizzoli has to result in other methods to find out what happened. Howvever, Rizzoli is distracted when her mother, Angela, sets her up on a date.
A student is killed during the day and the case shows that the girl murdered had more secrets to tell. Angela gets into an argument with Frank, Rizzoli's father, over a the old car.
When the oldest brother of a Boston "Brahmin" family is found dead in the harbor after a sailing accident, Rizzoli has doubts that it wasn't murder. Maura is close to the family and Rizzoli makes her resentment known when Maura's "friends" try to ruin the investigation. Angela tries to start a new thing and sells Polynesian Health Juice.
After a woman is beaten and killed outside a Lesbian bar, Rizzoli and Maura automatically tail it as a hate crime. Going undercover, Rizzoli hopes to draw out the killer. Meanwhile, Maura sets Rizzoli up with her Yoga instructor for a night on the town.
When Rizzoli and Maura decides to run for the Boston Marathon, they have to, instead track down a killer when one of the runners is found murdered. Instead of trying to cancel the race, Rizzoli thinks that it is best to simply let the runners run and find the killer amongst the crowd.
When a body is discovered in a park, Rizzoli and Maura discover that Charles Hoyt, a serial killer who tried to murder Rizzoli, is out and at large. Maura tries to find what Hoyt is up to while Rizzoli tries no to panic.
A man with no identity is found murdered with an ice pick, Rizzoli is lead into the past of the Irish Mafia. When she discovers something crucial about the man, Maura is sent on a personal quest. Frankie Jr. tries to help his father with getting more customers.
After a undercover cop is killed, the killers are forced to get into the Boston Police Department and take what he had on him. This leaves Rizzoli, Maura and Frankie Jr. trapped inside the station. After Frankie is shot, Maura races to save his life. Guest stars: Chazz Paliminteri and Erik Palladino
After getting shot in the stomach during last season finale, Rizzoli is awarded with a medal for her bravery and hailed as a hero. However, when a car bomb kills a decorated soldier, Rizzoli and Sgt. Colonel Casey Jones work together to get the killer before it is too late.
Rizzoli and Maura relax at an outdoor spa, but it is interuppted when they find a pregnant woman, who was a surrogate mother, has been found murdered. They race to see if they can find the biological parents.
A young woman is found dead after sailors party on the streets of Boston during Fleet Week. Barry's father comes to town and Barry is tense through the entire ordeal. Meanwhile, Maura goes on a date with Angela's mechanic and Rizzoli is a little uneasy.
A girl, who is the daughter of an undercover police officer, is kidnapped and the entire police department is on it to find the girl before it is too late. When a girl is found dead in the woods, Jane fears the worse when she sees the body.
Jane and Maura are called when a member of the coaching team of the Boston Pilgrims baseball team is found dead. What looks like a accident, turns out to be more then that. After the death of their Star player, things get worse. Jane's brother Tommy comes home finally.
A killing at the site of a Revolutionary War reenactment puts Maura on the front lines of the investigation, as she must tap into her considerable knowledge of American history to crack the case. Elsewhere, Maura's mother (Jacqueline Bisset) arrives for an art exhibit. Richard...
Jane and the team investigate what appears to be a modern-day witch hunt in Salem. Meanwhile, Frankie's old girlfriend returns to town with a surprise, and Jane has no problem speaking her mind about the situation.
Jane and Maura delve into a family's background when a man is killed in what appears to be a mugging gone wrong. Meanwhile, a romantic and mysterious figure from Maura's past shows up, causing a rift when Jane suspects Maura is hiding something.
The team investigates the death of a female dockworker in a case that comes with mob connections and possible revelations about Maura's biological father. And as Jane attempts to dodge sensitivity training, Maura inches closer to Jane's brother.
The gal pals snoop when a young man is killed in a jail bathroom just as he was to be released from prison. Enter sinister serial killer Charles Hoyt (Michael Massee), who claims to have the inside scoop on the slaying. Meanwhile, Frankie Jr. gears up for the detective's exam.
When a community activist is gunned down, one brave witness comes forward to testify against a well-known gang member who is thought to have murdered 15 people. While the detectives work diligently to put him away, television host Bill O’Reilly comes to town for a book signing and criticizes the police department on-air. Roselyn Sanchez guest-stars as the gorgeous-and-driven Assistant District Attorney Valerie Hudson.
Boston Homicide teams up with the FBI after a bank manager is shot during a robbery. Jane’s brother Tommy (guest star Colin Egglesfield) may be facing more trouble just as his relationship with Maura begins to grow. Tessa Thompson guest-stars as by-the-book FBI Agent Anna Farrell, who has a complicated history with Detective Frost.
Jane attends her high school reunion and brings Maura along for the ride, but the fun is cut short when one of her old classmates turns up dead on the football field. Jane must focus on the past when she realizes everyone in her class is a potential suspect. Meanwhile, Korsak gets a visit from ex-wife Melody Patterson (guest star Lolita Davidovich), who hopes he’ll invest in her new business. Chris Vance returns as Sgt. Major Charles “Casey” Jones, an old flame of Jane’s, and Matthew Del Negro guest-stars as Angela’s car mechanic, Giovanni, who once had eyes for Maura.
The world of competitive dance turns deadly when the mother of a star performer is stabbed to death at a competition. Jane and the team search for clues, but they soon realize something is off about the woman’s history. Korsak has his hands full when his stepson is accused of shooting a cop. Guest star Lolita Davidovich returns as Korsak’s ex-wife Melody.
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. Guest star Billy Burke returns as FBI Agent Gabriel Dean, who hopes to rekindle his relationship with Jane. And guest star Jacqueline Bissett reprises her role as Maura’s mother, Constance Isles.
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.
Tensions continue to mount between Jane and Maura, causing those close to them to be caught in the middle. But they must put aside their differences when they investigate the case of a college student who died in a tunnel. Meanwhile, Frankie Sr. returns with news that upsets Angela.
When Maura meets a new guy named Dennis in a very unusual way, he opens up a different side of her. And Jane is filled with mixed emotions after someone from her past returns.
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 Davis. Angela gets involved in a political campaign. And a nun from Jane and Frankie Jr.’s past returns.
When a rich financier is found stuffed in a trashcan wearing a cloak and mask, Jane and Maura must figure out what happened. Meanwhile, Maura makes a deeper connection with her biological mother, Dr. Hope Davis, and half-sister, who still doesn’t know Maura is related to them.
The ladies probe the killing of a husband and wife who were psychiatrists. Soon, an attendee of a medical-examiners seminar offers to help Jane and Maura in the case. Elsewhere, the Rizzoli family realize they may have connections to a pregnant stranger.
A bride is killed right before she walks down the aisle, and Jane and Maura must figure out if the groom’s ex-girlfriend is a suspect, or if there’s a deeper connection to the bride’s European roots. On the homefront, Jane has a new neighbor who captures the attention of Angela, Frankie and Frost.
A boy band star returns to his roots for a show and winds up murdered. Jane and Frankie, who grew up with the victim, work hard to solve the case. Meanwhile, Jane and Maura must decide if it’s time to tell Angela the truth about Lydia’s pregnancy just as Angela prepares to throw her a baby shower.
When a statue breaks open to reveal a dead woman inside, Jane and Maura must find the killer quickly as the body count begins to rise. Back at headquarters, a new homicide detective is named to the squad. Meanwhile, Dennis Rockmond returns to Boston after disappearing on Maura and tries to woo her back. Lydia goes into labor.
When a man having breakfast in the Division 1 Café dies from poisoning, Jane and the team must quickly find the source as Angela and the irascible Stanley both come under scrutiny. Meanwhile, Tommy wants proof that he’s the biological father of Lydia’s baby as she returns to take the baby back. And Detective Korsak is reunited with one of his ex-wives.
Jane and Maura investigate the apparent suicide of a notable young author of memoirs. Meanwhile, Frost grows obsessed with a past case, and Jane unearths information about a secret romance involving Angela.
The virtual world and the real world collide when a microbrewer is killed. Angela tries to move on from a failed romance by seeing someone new. And Jane and the team begin to mentor underprivileged teenagers, a move that ends in near disaster.
When a former college football player is stabbed inside a carwash during a fundraiser for his alma mater, Jane, Maura and the team must piece together clues to track down the killer. Meanwhile, Frost's mother visits Boston with some unexpected news. And Lt. Col. Casey Jones bumps into Jane and is forced to reveal some startling news of his own.
Dr. Hope Martin returns to ask Maura for a life-altering favor. Jane worries about the impending spinal surgery for Lt. Col. Casey Jones, and Tommy shows off baby T.J. But all gets shoved to the side when a building collapses, trapping loved ones inside.
A community parade turns deadly in a case that brings family tensions and politics to the forefront. Maura, who is dealing with her own family issues, is not quite herself. And a surprise visit from Lt. Col. Casey Jones (guest star Chris Vance) reveals some shocking news.
While investigating the homicide of an overzealous journalism student, Jane is not happy when a former colleague returns to BPD as the new lieutenant of the drug unit (guest star Amaury Nolasco). But the murder she’s investigating soon forces her to deal with him – and the event wrecked their relationship. Meanwhile, an alarming tip from Cailin (guest star Emilee Wallace) causes Maura to investigate Hope (guest star Sharon Lawrence).
Maura becomes the key suspect in a homicide case when Maura’s date turns up dead – and Maura can’t remember their evening together. As the shocking evidence against Maura piles up, Jane struggles between protecting her best friend and doing her job.
On the first day of Paddy’s (guest star John Doman) murder trial, Maura gains insight into her father from Hope (guest star Sharon Lawrence). Korsak opens up about Cavanaugh’s tragic past. And in an unexpected twist, Maura must decide which side she’s on when she and Jane unravel a shocking secret about Paddy and Hope that affects them all.
TJ's christening turns grim when a body is discovered in the church. Jane almost abuses her power in order to protect Tommy when Lydia's fiancé, Stuart Stawbridge (guest star Jareb Dauplaise) threatens to take custody of TJ, and budget cuts cause tensions to run high around the department.
When a beleaguered Jane spills hot coffee on a stranger at Boston Joe's, a viral video of Jane’s bad day potentially jeopardizes her career and reputation. Meanwhile, the squad rushes to solve a puzzling murder case involving a conspiracy theorist.
A popular high school teacher is killed in a hit and run that is clearly no accident. The squad works to solve the case, but Jane is preoccupied with Lt. Martinez’s (guest star Amaury Nolasco) apparent favoritism towards his own drug unit.
Frankie Jr. is brought in to help with a gruesome murder case involving a youth hockey league. Frustrated with Hope (guest star Sharon Lawrence), Cailin (guest star Emilee Wallace) asks to stay with Maura. But Maura quickly learns that living with a teenager requires skills she does not have.