The pieces of a dismembered body are found lying in a purple pool of water, except the head is missing. The team finds that the body belongs to Jared Addison, a science fiction writer who had several mental problems. With Sweets' help, several suspects are hunted down, however the team has trouble finding enough evidence with the victim's head still missing.

Booth and Brennan go to investigate a body found in the Chesapeake Bay. After arriving, they find only the upper torso, giving the team little to work with other than remnants of the victim's breast implants. Brennan and Booth are led to a small church in Maryland, where they find that the victim was a pastor. When the team finds the lower half of the body, they learn that their initial assumptions may not been incorrect.

When the smashed remains of a well known artist are found in an impounded junkyard car, Booth and Brennan are on the case to find out if foul play is to blame for his death. With suspects ranging from the artist’s rival to his own assistant, the team must race

against the clock to find evidence of murder before the car is relinquished and put on exhibit as the sculptor’s ultimate display of self-sacrifice for the sake of his art.

While en route to China to identify prehistoric anthropological remains, Booth and Brennan are called upon to solve a murder in midair when the flight attendant discovers a fully cooked human body in the plane's microwave.

Brennan's father Max lands a teaching position at the Jeffersonian. When he ends up helping out with the murder case at hand, Brennan is noticeably bothered by his sudden presence in her professional life.

A shallow grave holds the remains of conjoined twins; Booth and Brennan infiltrate a circus community after they discover that the twins were jugglers there.

When a volunteer fireman is murdered at an ice rink, Booth and Brennan begin the investigation, but Booth must excuse himself due to a conflict of interest. When details come to light, Booth becomes a suspect in the homicide.

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

The team investigates a sci-fi convention when a woman in a medieval princess dress is found murdered. With Booth's back injured, Agent Payton Perotta steps in once again to help

When newlyweds encounter a corpse while bungee-jumping off of a bridge, Brennan and Booth are sent to investigate. After determine the cause of death was not suicide, the team at the Jeffersonian discover an unknown substance coming from the body. This sends the lab into lockdown and have only 24 hours to uncover the murderer before the body disintegrates.

The body of a pregnant 16-year-old athlete found buried in a mound of salt in a city de-icing truck leads Booth and Brennan to the discovery that many of her teammates are pregnant or have babies after a pregnancy pact.

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 and Brennan are sent to investigate when human remains are found during a photo shoot. When the team uncovers a meteorite in the victim's ear, they are led to the Collar Institute of Science in D.C.

When it is discovered that a stage prop used by a Norwegian death metal band is in fact a real human skeleton, the remains are sent to the Jeffersonian when authorities determine the victim was an American citizen.

When a Jeffersonian coworker dies of heart failure, the entire team goes to the wake where, upon viewing the body, Brennan realizes the death was no accident.

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.

When a human body is found inside the strung up Otter mascot uniform of a rival school, Brennan and Booth investigate whether the body inside the costume was dead beforehand, or killed during a Middlesex University bonfire event. The body is identified as Jimmy “Beaver” Bouvier, a fraternity brother at Middlesex University. When Brennan and Booth question his fraternity brothers, they learn that Beaver had a money-making operation on the side and was making a killing of his own. Meanwhile, Booth offers to help his brother Jared find a new job after being dishonorably discharged from the Navy.

The team is on the case when human remains are found inside a barrel of wine during a wine tasting. When the victim turns out to be a wine critic whose scathing reviews were capable of sending a vineyard to its ruin, everyone from the winery's owner to the victim's own wife becomes a suspect.

In the season finale, a dead body is found at a club called "The Lab." The team has to do some unexpected and unusual things that have to do with this club. Brennan and Booth may become a couple.