Season 5 was renewed on August 15, 2013. The season consists of 18 episodes which premiered on June 17, 2014 and reached a hiatus with the broadcast of the 12th episode on 2 September 2014. The remaining 6 episodes were broadcast in February.
A woman is stabbed to death while jogging in a park. The investigation is stepped up when an empty baby stroller, believed to have contained her baby, is found nearby. The baby's father, the woman's ex-husband, is questioned, but he was stuck in traffic with his new girlfriend at the time of death. However, a camera at a gas station shows otherwise for the girlfriend's alibi. She was not in the vehicle. The father is complicit, but he reveals the baby was taken to a church. Meanwhile, Frankie and Maura decide they are too much like family to pursue a relationship; Jane deals with morning sickness while unsuccessfully trying to hide her pregnancy from her mother; and the team is called to a car accident that claimed the life of Detective Frost.
While the team deals with their grief in order to make arrangements for Frost's funeral, a young woman with amnesia wearing bloody clothing walks into the precinct holding a gun and stating she might have killed someone.
Loners, who would not be missed for extended periods of time, are interviewed to work on a farm. Unfortunately, those hired are killed by the disgruntled son of a bankrupt farmer, which culminates in a tense shoot-out that puts Jane and her unborn child at risk. Meanwhile, she finally confirms to her mother of her pregnancy, which Angela already knew, and accepts Maura's help, which comes with constant prenatal advice.
A survivalist is believed to have died from halomethane poisoning in his protective fallout shelter, until Maura deems the death "suspicious" since alternative methods to the gas exist today. The team investigates the victim's means of survival if he were to have exited the shelter after a catastrophe. Meanwhile, Angela asks Jane to find out why Frankie is being secretive, but Jane wishes to know the same about Korsak.
A wealthy woman with terminal cancer prepares to commit suicide but is killed before she is able to do so. The team investigates her family and staff, both past and present. Meanwhile, since Maura must teach a college forensic science class, Angela becomes responsible for Jane, who considers her mother's help as meddling. Maura then takes a liking to a professor but remains cautious, due to her luck with men. Also, the void left at Frost's desk forces the team to make a decision.
Judith Barnett, a woman who recently lost a lot of weight, is initially thought to have been stabbed to death in her home. Her husband Alan feared her weight loss would make her more attractive to other men, including their handyman, Luis Benitez. His knife is found near her body. With Maura at a convention, the team must rely on her Assistant ME Susie (Tina Huang) to use her quirky methods to help find the murderer. Meanwhile, Korsak reminisces about the death of an old musician friend, whose grandson has contacted him to play some of their music.
The mysterious murder of a used-book dealer leads to one suspect with ties to Paddy Doyle. When Jane questions Paddy about the case, he requests to see Maura, who agrees upon learning he is being transferred to a California maximum-security prison. Meanwhile, Angela decides to start fresh with her life, which includes breaking up with Lt. Cavanaugh and quitting her job at the café.
When a young woman is murdered by a contract killer, Jane must put herself at risk to save a teenaged witness, named Tasha, as the team scrambles to find her. Meanwhile, Korsak adds crime scene analyst Nina Holiday (Idara Victor) to his team.
The team investigates the poisoning death of a woman found mummified in a wine cellar. While Jane recovers at the hospital from her wounds sustained in protecting Tasha, she learns that she lost the baby and that Tasha will be placed in a group home upon leaving the hospital.
An old friend of Korsak's dying in prison asks him to solve the case that put him there – the deaths of his wife and daughter killed in a house fire 15 years earlier. Korsak's sense of urgency causes him to take the case file to Maura's house, where Jane, awaiting medical clearance to return to work, steals information from it to help solve the case. Meanwhile, Angela secretly keeps the mail from Jane that contains her clearance letter.
When tenants complain of water leaks, a landlord finds the body of a man half-submerged in a bathtub. Initially, it is believed Richard Nelson did so to escape the sweltering heat outside. During autopsy, Maura discovers Nelson died of strangulation. His financials reveal him to be a millionaire. Although Nelson told everyone that he found the money while jogging, the investigation shows him to have been involved in a kidnapping. His accomplice killed him, thinking he kept the ransom for himself. Meanwhile, Angela drinks some tea to stay cool, but it has amorous side effects; and Korsak intends to find the owner of a lost dog, even though he names it and gets used to it.
A county prosecutor appears to be framed for a murder, but proving his innocence puts Jane in danger. Meanwhile, Angela takes it upon herself to teach Maura about children's interest when she learns Maura is to meet Jack's 12-year-old daughter.
After Jane saves Paul, the prosecutor, when he jumps from a bridge, the squad resumes searching for the real killer. Meanwhile, Angela asks Frankie for help in preparing for a restaurant-manager job interview. Korsak buys the local bar as a retirement present for himself.
Jane and Maura investigate the death of a victim that they don't know, as the only body part that they find is a foot; while Angela, who is frustrated with not being able to find a job, ends up getting a job at the bar, by giving advice to a man about proposing to his girlfriend and the woman who delivers the beer.
The owner of Mamaki Clothing is thrown from his business' balcony, but his death occurred before that. The offices reveal a burglary, in which only files are taken. Corporate espionage is the apparent motive. However, the owner's wife also goes missing, and the team finds themselves working with a private detective who had been caught snooping by the victim just before his death. Meanwhile, Maura cautions Angela about spending her new income, and Frankie asks Jane's help in focusing on his firing range test.
After his wife reports him missing, Todd Reynolds is found beaten to death outside his seemingly disabled vehicle. After questioning his son Logan, the team searches for a man Todd was heard arguing with, two days ago. Maine Detective Mike Guthrie arrives to suggest they are looking for the same person who killed a "stranded" 60-year-old woman. Jane records Mike's voice, and Logan confirms his is the voice that was heard. Korsak finds a connection between Mike and Todd from the days they attended summer camp together, where Mike was teased for bed-wetting. Meanwhile, Maura becomes a victim of identity theft.
While the team investigates a string of sniper attacks in Franklin Park, Maura must elicit a statement from an injured witness believed to be having a psychotic break, to the extent that he believes himself to be a werewolf. She also must cope with her ending her relationship with Jack.
A man dies while role playing with his wife in a Boston hotel room. His death appears to result from a fall, but Maura, after accompanying Jane to a resort, has several epiphanies – one of which is that someone else could have hit the victim on the head, since an object swung with great force was the only way the head injury could have occurred. Meanwhile, Tasha is applying at several colleges and wants to get accepted on her own merit, not Maura's pulling strings. A local university, BCU (Maura's fictional alma mater Boston Cambridge University) accepts, but their offer of financial aid is insufficient. When Maura learns this, she works with Korsak and the team to help Tasha attend "BCU" by awarding her the newly created Barry Frost Memorial Scholarship.