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.
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. Meanwhile, Maura learns why Casey is staying away from Jane.
The detectives investigate the murder of a psychiatrist couple. A medical examiner attending a seminar offers to help Jane and Maura. A pregnant stranger may have something in common with the Rizzoli family.
A boy band star that Jane and Frankie grew up with returns for a show and ends up murdered. Jane and Maura try to figure out whether it's time to tell Angela the truth about Lydia's pregnancy, especially since Angela is planning to throw a baby shower.
When a man dies a suspicious death after eating breakfast in the Division One Cafe, Jane and the team search for the source. Korsak bumps into one of his ex-wives during the investigation. Meanwhile, the Rizzoli family have to decide whether they should fight for Tommy, Jr., who could still be Frank's, when Lydia takes him away.
While the homicide squad observes "health week", the team investigates a famous author's staged suicide. Meanwhile, Frost decides to review an old murder case, and Angela's new romance isn't a secret anymore.
Dr. Hope Martin returns to ask Maura for a life-altering favor. Jane worries about Casey's upcoming spinal surgery, and Tommy shows off baby T.J. But all gets shoved to the side when a building collapses, trapping loved ones inside.