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.

When the remains of a couple are discovered in a cave at National Park, the team must piece together the identity of the man and the woman as well as solve the crime. After interrogating two viable suspects, the team identifies the woman as a marketing executive who also served as her partner’s AA sponsor, providing clues that lead them to expose the truth. Meanwhile, Booth’s girlfriend and Afghanistan war correspondent, Hannah Burley, makes a surprise visit. After meeting Burley and sensing the couple’s genuine happiness, Brennan re-evaluates her own relationship with Booth, and he tries to teach her that love is not always logical.

When Booth and Brennan are called to investigate decomposed remains found at the Jersey Shore, the team IDs the victim as Richie “The V” Genaro, a 23-year-old who partied the night before at a popular nightclub. Booth and Brennan question Genaro’s peers and the club bouncer, and Brennan surprisingly proves her pop culture savvy and anthropological expertise after watching what she believes to be a documentary on the inhabitants of the Jersey Shore, but was in actuality a reality show set there. Meanwhile, at the lab, the team grows fond of Booth’s girlfriend, Hannah, and Angela tries to keep her pregnancy a secret.

After a skull and decomposing hands are found in a dumpster, the team must not only solve the crime but also search for the rest of the victim’s remains. Identified as Ray Raminsky, the victim turns out to be a bounty hunter in search of Charles Braverman, a man indicted for the murder of a co-worker. Meanwhile, Brennan is asked by Professor Bunsen Jude “The Science Dude” (guest star Grier) if he can shoot an episode of his children’s show from The Jeffersonian Lab with Brennan as his special guest. Brennan initially turns him down, but is surprised when he makes her a deal she can’t refuse, so she takes him on as a new “squintern.” As the team pieces together the details of the crime, they discover that they are not alone in the hunt for Braverman and find themselves in a chase with an unexpected suspect.

After the skull of a promising young dancer is found lodged in concrete at a construction site, the team must first figure out what happened to the victim’s skeletal structure. After learning the victim quit ballet to pursue hip hop, Booth and Brennan uncover another layer of evidence that points them to a suspect who had a secret relationship with the victim. Meanwhile, when Hannah is put on assignment in a dodgy part of town, her safety is jeopardized and her life is put in critical danger.

The past and present collide when human remains from a 150-year-old slave ship, the Amelia Rose, surface. The team is tasked to give the deceased a proper burial but make an unforeseen discovery linked to a recent murder. In the course of the investigation, Booth and Brennan are led to a different kind of ship - a "Cougar" cruise - where they learn their victim was seen moments before his death. Meanwhile, Sweets struggles to maintain a casual relationship with Daisy, and Cam discovers a surprising and emotional connection to the Amelia Rose.

An event for a candymaker (Wayne Knight) turns bitter when human remains are discovered in the world's largest chocolate bar; Cam struggles with her daughter's decision to attend a college that fails to meet her high standards.

Booth and Brennan’s next case leads them to a crime scene where a human carcass has literally melted into the dashboard of a charred truck. As the team investigates the case, they discover a gunshot wound in the victim, but learn that neither the fire nor the bullet was the cause of the victim’s death. Additional clues lead them to a local high school where the victim’s wife is a teacher. As a student-teacher relationship begins to surface and a pattern takes shape in the lab, the team is able to track down the murder weapon and solve the crime. Meanwhile, Sweets resists the temptation of allowing his feelings for Daisy to interfere with helping her pass a government psychological evaluation, and Hannah attempts to break the ice and warm up to Booth’s son Parker.

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.

An unidentifiable body is discovered in the shower of an upscale home belonging to a young female socialite. With the help of nosey bones expert and Jeffersonian “squint” Clark Edison, skeletal reconstruction and evidence in the drain reveal that the victim was a young girl employed by a counterfeit handbag distributor. The team learns that the victim supplied counterfeit purses to her socialite acquaintance, and after interrogating the self-centered socialite and sifting through footage on a hidden camera, they discover evidence linking them to the murderer. Meanwhile, Angela and Hodgins discuss their future home and where they want to raise a family, and Booth opens up to Hannah about Brennan’s feelings for him

The city anxiously anticipates the arrival of Heather Taffet, more notoriously known as "The Gravedigger," for her final appeal after being sentenced to death for a kidnap-murder and a series of similar coldblooded crimes. But when a bullet targeted at The Gravedigger is fired from a distance and hits her, the Jeffersonian team is tasked to piece together the sniper's precise location as well as identify the suspect and his motives. With the help of probing investigator Caroline Julian, Booth and Brennan put together a list of likely suspects, but the evidence and the remarkable skill needed to pull off the crime leads the team to believe that the crime was an inside, professional job, leaving Brennan's father Max and even Booth as plausible suspects. Meanwhile, Sweets attempts to put on a brave face after being caught in the firestorm just moments following a chilly encounter with The Gravedigger.

A body disguised as a scarecrow is found with a bullet wound in a remote cornfield, and the team is forced to work against the clock to avoid a storm and potential complications that would affect the evidence. Booth and Brennan interrogate the victim's three wives, who are also sisters, and learn that jealousy between the sisters and their desire for their husband's attention had caused a major rift in the family. Booth and Brennan also question one relative who disapproved of the victim's polygamy. Meanwhile, Cam loses confidence in her relationship with her on-call doctor boyfriend, but they both realize they need to make their relationship a priority.

A BMX rider’s remains are discovered on the roof of a warehouse after a failed bike stunt. While Booth and Brennan interrogate the victim’s fellow riders, Hodgins and newly mellowed “squint” Fisher identify the numerous fractures in the victim’s skeletal structure, and Angela recreates the series of events that led to the fatal accident. Meanwhile, Sweets turns to Booth for advice about his relationship with Daisy, and Booth makes a decision about his relationship with Hannah.

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.

Sniper Jacob Broadsky takes out a victim who escaped from the justice system; Booth uses his military training to try to stop Broadsky before he strikes again; Angela's father visits the Jeffersonian.

During a blizzard that causes a citywide blackout, the team must solve a murder case that could be connected to a possible viral outbreak; Sweets starts a touchy conversation about Brennan and Booth's relationship.

The remains of a mythbuster television show host are found in the wilderness appearing to have been killed by the mythic Chupacabra, a reptile-mammal hybrid creature whose existence has not been confirmed. The team soon learns that the victim traveled to the remote West Virginian area to debunk the Chupacabra myth, and they interrogate possible suspects, including a rival wilderness-channel host/cryptozoologist/pet psychic. But when a tape is recovered at the crime scene and peculiar tooth marks are found in the victim's remains, the team learns details about the victim's demise that challenge the original theories surrounding his death. Meanwhile, recovering alcoholic squint Vincent Nigel-Murray makes amends with each member of the team and makes some surprising confessions.

The remains of a maritime museum security guard are found in the Florida Everglades after an attempt to steal an obsolete 17th century nautical chart fragment used to find treasures. In order to solve the crime, Booth seeks out Walter Sherman, a former Iraqi soldier with an uncanny gift to unearth anyone and anything. With Sherman's help, as well as that of his colleague, Ike Latulippe, and his legal advisor, Leo Knox, the team is led to tattoo artist who points them in the direction of a tough young woman. But when the woman is found murdered with remnants of the map lodged in her remains, the team discovers centuries of history linked to the map and the suspect behind the crimes. Meanwhile, Brennan puts Sherman's remarkable skill to the test, and Booth harbors cold feelings toward his former military comrade.

The team identifies the remains of a successful ad man found in the grounds of a newly built community center playground. Upon inspecting the victim’s home and interrogating his former partner and employer, Booth and Brennan discover that the victim burned bridges by adopting an aggressive attitude toward honesty and was a member of a radical honesty support group. Meanwhile, each of the team members attempts to adopt a more honest way of communicating that doesn’t always lend itself to good relationships, and Angela urges Hodgins to confront the realities of their pregnancy

When a 15-year-old Jane Doe is found on the streets, it is up to Brennan, Jeffersonian Intern Arastoo Vaziri and the entire Jeffersonian team to figure out her history and if she is responsible for a recent murder

Rogue sniper Jacob Broadsky returns once again, claiming another victim and making Booth determined to put him away once and for all.

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.