After a skull smashes into the windshield of a teenager's car, the investigation reveals the skull has been gnawed on by human teeth, which implies cannibalism and marks the beginning of the Widow's Son case. Meanwhile, Angela and Hodgins hire a private investigator to find her husband. Bones searches for Zach's replacement and the team gets a wonderful surprise.

A woman's car is run off the road and she is killed, but her baby miraculously survives the accident. Booth and Brennan go to the woman's hometown to try to find out who's responsible for running her car off the road. Bones, with help from Booth, takes care of the baby until the team finds out who killed the mother.

Season four begins all the way in England, with Booth speaking at Scotland Yard and Brennan guest-lecturing at the prestigious Oxford University. Knowing of Booth and Brennan's expertise in their respective fields, local officials ask for their help with a high-profile murder investigation that involves a British heiress.

With the case of the murdered heiress solved, Booth and Brennan prepare to head back home, but are shocked to learn of another murder - and this time it's someone they know. Meanwhile, with Birimbau unexpectedly coming back into Angela's life, things get complicated between her and Hodgins.

While trapped and trying to escape from a ship in the middle of the ocean, Booth is haunted by strange hallucinations.

When the half-eaten body of Cam's former fiancee is found in the tiger cage at the zoo, Booth and Brennan uncover that his death was far from accidental. Now the team must put the pieces of the fiancee's final day back together, including hypnotizing a suspect in order to spark his memory.

Booth's detective friend from Tokyo, Ken Nakamura, calls him when his sister, Sachi, goes missing while in Washington, D.C. With Brennan, Booth investigates her disappearance.

It's been six weeks since Booth and Brennan have seen each other. Booth has been recovering from brain surgery, and Brennan has been on a dig in Guatemala. Angela's psychic, Avalon Harmonia reveals while reading Angela's tarot cards that there are multiple bodies buried under a Washington,DC fountain. Angela shares the information with Brennan and Booth, but they're both a little skeptical. The lead pans out, and the duo find the remains of 11 bodies exactly where the psychic said they would be. Meanwhile, Sweets has certified Booth mentally fit to return to duty after his brain surgery, but Booth is still experiencing some side effects from the coma.

Brennan and Booth investigate a set of uniquely disfigured remains allegorizing biblical text. As they acquire more information about the victim, a former patient of Dr. Adam Copeland at Havenhurst Sanitarium, they are confronted with suspects who are hard to characterize as either good or evil. Meanwhile, Jeffersonian intern Arastoo Vaziri reveals a secret about his past.

The team works to uncover clues buried under a life’s worth of possessions saved by a hoarder in order to solve the mystery of his death. Meanwhile, Angela’s father has a specific purpose for his most recent visit, and Brennan and Booth are confronted with unique opportunities.

With Cam’s reputation and career on the line, the team travels from overseas to help her solve the case of an unidentified young boy. The Forensics Anthropology Unit lost much of its vigor after disbanding to pursue personal ventures, and it will take the collaborative energy and knowledge of the newly reunited team to unravel evidence and find closure for the family of the unknown boy. After unearthing new clues in the lab and making unexpected personal discoveries, the team realizes they belong back in Washington, D.C.

Brennan gets a glimpse into her own life when the body of a brilliant and career-driven surgeon is found in a rough neighborhood with multiple fractures in her skull and no indication as to how or why she was there. While the team investigates the case objectively, Brennan struggles to separate her own life from the victim’s as she perceives many parallels between them the more she learns about the victim’s past. Meanwhile, evidence found at the crime scene brings the team closer to solving the case, but it’s Brennan’s unique perspective that propels her to retrace the final events of the victim’s life. With the reassurance of a new friend and Jeffersonian security guard, Micah Leggat, Brennan makes a discovery about herself and learns a lesson about taking chances.

The liquefied remains of a wedding planner are found in her home tanning bed on Valentine’s Day, and Cam pressures her team to solve the case in time so she can celebrate the holiday with her boyfriend. While the “squints” works tirelessly in the lab, Booth and Brennan interrogate a slew of possible suspects until they unlock classified files in the victim’s computer, which lead to their main suspect. Meanwhile, Booth and Brennan downplay the significance of Valentine’s Day, and Hodgins tries to plan a romantic day for Angela, but “squint” Clark helps him realize that the most meaningful gifts come from the heart.

In the 6th season finale, the team investigates the disturbing, unidentifiable remains of a bowler that were found jammed in one of the bowling alley's automatic pinsetters. After hitting a dead end in the case, Booth and Brennan decide to go undercover and join a competitive bowling team in search of answers.

The body of a woman found buried under a paintball field yields more questions than answers as the investigation into her death reveals even she didn't know who she was. On the domestic side, Booth and Brennan adjust to sharing space with each other… and her growing stomach.

A cryptic message penned in human blood is discovered at a national monument. As the Jeffersonian team embarks on a scavenger hunt to solve the case, they realize their tech-savvy suspect remains one step ahead of them. Meanwhile, Booth and Brennan search for the perfect home for their new family.

Having been accused of murder, Brennan is on the run from the FBI, with help from her father Max. Booth and the Jeffersonian team are convinced evil tech genius Christopher Pelant has manipulated key evidence in the case to pinpoint Brennan as the prime suspect. Then, an anonymous tip leads the team to the remains of a high school guidance counselor that may hold the key to proving Brennan's innocence.

A street artist who is plastering his work on a billboard falls into his glue—and onto a corpse—so the team try to get him unstuck from the remains as they also work to identify the body. Meanwhile, Booth takes a stab at stand-up comedy at a club's open-mike night to look for suspects; and Angela finds herself attracted to the street artist.

Brennan and the team attempt to absolve Booth and get him released from prison. The remains of a man who has been dead for over sixteen years prove to be significant.

The team investigates a body found in a car crash, the remains of which belong to a founder of a men's rights organization who may have been the victim of domestic abuse. As Brennan learns more about the tenets of the victim's organization, which claims middle-aged white men are oppressed and feminists are man-haters, Brennan uncharacteristically loses her cool during an interrogation and assaults the organization's co-founder. Meanwhile, Angela and the team struggle to deal with Hodgins post-wheelchair bitterness and Booth is convinced Brennan is a jinx for the Philadelphia Flyers.

The team investigates the death of a popular professional hockey player whose headless corpse was dumped in the river. As Booth and Aubrey question the player's coach, Booth's depth of hockey knowledge is integral to solving the case, and he's reunited with a hockey rival from his past, putting him back on the ice once again to face off against him. Meanwhile, Hodgins and Oliver have a competition of their own when Hodgins builds two drones and they compete to retrieve the victim's missing head, and Booth and Brennan attempt to declutter their home.

After discovering the body of a man involved with creating artificial intelligence bots, the team must figure out whether the victim's own A.I. bot was programmed to kill him. In the meantime, Bones plans a special surprise for everyone for her 40th birthday.

Brennan testifies for Zach in trial, Angela reveals some big news, while Aubrey and Jessica come to terms about their future together. All the while, the team discovers Kovac has escaped, leaving Booth in a race against the clock to protect himself and those closest to him from what may be Kovac's most dangerous plan yet.