Jane and Maura investigate after the coach of the Boston Pilgrims baseball team is found dead in the locker room. The death comes as a star player and the team owners battle for control of the team. Meanwhile, Jane's brother Tommy returns home after being released from jail.

When a young dockworker is found dead, the team discovers that there are mob connections; Jane tries to avoid sensitivity training; Maura starts spending time with Jane's brother.

Boston Homicide teams up with the FBI after a bank manager is shot during a robbery. Jane’s brother Tommy 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.

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 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.

Dr. Hope Martin returns to ask Maura for a life-altering favor. Jane worries about the impending spinal surgery for Lt. Col. Casey Jones (guest star Chris Vance), and Tommy shows off baby T.J. But all gets shoved to the side when a building collapses, trapping loved ones inside.

A body is discovered in the church at TJ's christening; Jane almost abuses her power to protect Tommy; Lydia's fiancé threatens to take custody of TJ; budget cuts cause tension at the department.

A viral video of Jane jeopardizes her career and reputation; the squad tries to solve a murder case involving a conspiracy theorist.

A mock trial advisor dies during a competition. Meanwhile, Jane is concerned that Angela may be hiding financial issues.

A musician is stabbed in a bar; 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 poisoning; Tommy announces some big plans; Maura's birth mother tries to make amends with her daughter.

A senator's daughter is found murdered; Tommy begins to slip back into old habits; Jane reveals some shocking news.

A killer uses online ads to find victims; Jane discovers that it will be difficult to keep her pregnancy quiet.

A mortician's body is discovered in one of his caskets, leading the team into the world of embalming, interment and serial murder. Tommy Rizzoli visits with his son and considers returning to Boston. Jane's loved ones react to her news.