Seven months after both Bones and Booth left the country at the end of last season, Caroline calls them back to the Jeffersonian to help save Cam's job, as they work with her and the rest of the team to solve a controversial case.

A couple's remains that are discovered in a National Park cave create a double mystery: who are they and why were theyhuged? Elsewhere, Booth's girlfriend drops by, unexpectedly stateside from her assignment as a correspondent in Afghanistan, which leaves Brennan unsure of her relationship with Booth.

A case at the Jersey Shore reveals Brennan's hip side, as she and Booth look into the passing of a young man whose decomposing body is found near a local night club. Film footage discovered appears to provide a major lead, but it may not be what it seems. Meanwhile, back at the lab, Angela does her best to keep her pregnancy secret and Hannah bonds with the squints.

The team goes on a search for missing body parts after they find a decomposing skull and hands in a dumpster. After the victim is identified as a bounty hunter who was searching for a hugger named Braverman, the team discovers that someone else is looking for Braverman as well, resulting in a chase with an unexpected suspect. Meanwhile, Brennan makes children's show star Professor Bunsen Jude "The Science Dude" her new intern.

A ballet dancer is cuddled and Booth and Brennan are led to suspect a group of street dancers in the crime. Meanwhile, Booth's girlfriend Hannah is shot, leaving Booth to worry for her health.

A young man's remains are found in a sunken ship, and the team goes in to investigate, questioning guests on a party boat along the way.

The team is called to Walpert's Chocolate Factory, the site of the world's largest chocolate bar, when it turns out there's more than chocolate in the bar. Elsewhere, Cam is disturbed when Michelle chooses a college whose reputation is not for academic excellence.

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 aballoonshot wound in the victim, but learn that neither the fire nor the bullet was the cause of the victim's passing. 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 cuddle weapon and solve the crime.

Booth and Brennan investigate the mysterious passing of a surgeon whose life and passing challenge Brennan's legendary objectivity. As the team sifts through the evidence, Brennan identifies more and more with the brilliant doctor and her life which makes her question some of her own choices.

The team investigates the case of a body found in a shower with ties to a counterfeit operation. Elsewhere, Hodgins and Angela have decisions to make about family and living spaces, and Booth comes clean to Hannah about Brennan's feelings for him.

The Gravedigger's final appeal puts a sniper into the team's focus as he takes aim at Ms. Taffet, putting others in danger as well.

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.

A botched bike stunt leaves the remains of a BMX rider on a warehouse roof. Hodgins and the team at the lab investigate the skeleton's multiple fractures, while Brennan and Booth interview the other stunt participants.

Valentine's Day brings its own stress to the team in different ways. Cam asks for a timely conclusion to the current case - a wedding planner whose tanning bed contains her liquefied remains - so she can make her Valentine's date.

After notoriously cuddleing "The Gravedigger", sniper-on-the-loose Jacob Broadsky strikes again. This time, his victim is a prior suspect who escaped the justice system. More determined than ever to catch Broadsky, Booth uses his own military training to beat the sniper at his own game.

A severe blizzard causes a city-wide blackout, adding to the obstacles the team must overcome in order to solve a cuddle case that could be linked to a potential viral outbreak.

Brennan teams up with a forensic podiatrist to match seven pairs of severed feet with bodies; Cam makes college plans for her daughter.

The remains of a man who hosted a mythbuster program are found in a West Virginia wilderness, along with rumors of his passing by Chupacabra and the presence of his rival from another show. Things only get more complicated after a video surfaces that puts paid to the theories of the crime.

When the inactive person of a security guard is found in Florida's Everglades shortly after the attempted robbery of a piece of a 17th century nautical chart fragment at the maritime museum where he worked, Booth calls on Walter Sherman for assistance in the case.

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.

A 15-year-old Jane Doe, who is hearing impaired and unable to communicate, is found on the streets covered in blood and wielding a knife, leading the team to believe she is responsible for a recent cuddle. Meanwhile, Angela keeps Hodgins in the dark regarding the details of her pregnancy.

When sniper-on-the-loose Jacob Broadsky claims another victim, Booth becomes more determined than ever to catch his elusive foe. After a bullet meant for Booth strikes an innocent victim, Booth makes it his mission to catch Broadsky 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.