Angie Harmon and Sasha Alexander are back on the case as Rizzoli & Isles continues for a third explosive season. As the chart-busting second season came to a close, Jane shot Maura's estranged father, crime boss Paddy Doyle (guest star John Doman), as he tried to defend Maura against an assailant -- an incident which has driven a deep wedge between the two friends and colleagues.
Jane and Maura’s friendship suffers following the shooting of Maura’s biological father, gangster Paddy Doyle (guest star John Doman). Jane also finds herself in the middle of an Internal Affairs investigation. And her relationship with Agent Dean (guest-star Billy Burke) is exposed. Jacqueline Bisset and Ed Begley, Jr. also guest-star.
Tensions continue to mount between Jane and Maura, causing those close to them to be caught in the middle, but the two must put aside their differences to investigate the case of a college student who died in a tunnel. Meanwhile, Jane's father, Frankie Sr. (recurring guest star Chazz Palminteri - The Usual Suspects, Hurlyburly, Bullets Over Broadway), returns with news that upsets Angela. Recurring guest star Colin Egglesfield (Something Borrowed, Melrose Place) also appears.
When Maura meets a new guy named Dennis (guest star Eddie Cibrian - Third Watch, CSI: Miami) 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. Recurring guest star Chris Vance(Dexter, Burn Notice) appears as Sgt. Major Casey Jones.
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 (recurring guest star Chris Vance) was injured.
Jane looks for a way for Maura to meet her biological mother, Dr. Hope Davis (recurring guest star Sharon Lawrence - NYPD Blue). Angela gets involved in a political campaign. And a nun from Jane and Frankie Jr.'s past returns. Recurring guest star Matthew Del Negro (United States of Tara, Parenthood) appears as Giovanni and guest star Jenny O'Hara (Mystic River, Big Love, The King of Queens) appears as Sister Winnifred Callahan.
A man wearing a mask lounges in bed in a robe. A blonde woman wearing a mask comes in wearing lingerie. He's expecting her. He tells her he's "Rodium." He tells her not to be nervous, but she tells him she's been instructed. He's done this many times before. She takes out a syringe and injects him somewhere below. He starts to convulse.
At the offices of Drs. Rod and Eve Parker, someone all in black creeps in holding a gun. Eve walks out and is shot. Rod comes out and fights off the attacker but ultimately gets shot as well.
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 home front, 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 (guest star Alexandra Holden) 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 (guest star Eddie Cibrian) returns to Boston after disappearing on Maura and tries to woo her back. Lydia goes into labor. Colin Egglesfield, Daniella Alonso and Alexandra Holden also guest-star.
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.
A famous young writer of memoirs is found dead in an apparent suicide, but Jane and Maura soon discover there's more to the story. Meanwhile, Frost becomes obsessed with an old case involving a young African American student as his final appeal is denied. And Jane discovers Angela is involved in a secret romance.
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 (recurring guest star CHRIS VANCE) bumps into Jane and is forced to reveal some startling news of his own.
Dr. Hope Martin (recurring guest star SHARON LAWRENCE) returns to ask Maura for a life-altering favor. Jane worries about the impending spinal surgery for Lt. Col. Casey Jones (recurring guest star CHRIS VANCE), and Tommy (recurring guest star COLIN EGGLESFIELD) shows off baby T.J. But all gets shoved to the side when a building collapses, trapping loved ones inside.