After returning to Washington, D.C., renowned forensic anthropologist Dr. Temperance Brennan is called in by FBI Special Agent Seeley Booth to aid an FBI investigation involving a set of bones found hidden in a lake.
An SUV explodes outside a cafe, killing several civilians. When Dr. Brennan confirms the identity of the deceased driver to be the leader of the Arab-American Friendship League, the authorities suspect the man was a terrorist. After discovering the driver was murdered, Booth and Brennan try to find the murderer before he strikes again.
A boy is found hanging from a tree at an exclusive private school, apparently having committed suicide. Things quickly become more complicated when the school attempts a cover-up as Dr. Brennan and Booth must untangle a complicated web of sex, scandal and lies.
Dr. Brennan reluctantly joins Agent Booth to travel to Aurora, Washington State, where a human hand was found inside the stomach of a bear. As Brennan identifies the man, she discovers he might have been a victim of cannibalism. The investigation hits a roadblock when Booth loses a suspect in the woods, leading him and Dr. Brennan to spend some time in the local bar where Brennan is hit on by every available man in the small town. Booth shares a dance with Brennan to give her a break from all th
A six-year-old boy's remains are found near a shopping mall and when he is confirmed by Dr. Brennan to be the same boy who went missing from a local park, Booth and Brennan's team work together to find his murderer.
During a fight at a dance club, a wall breaks open to reveal a mummified corpse and a stash of methamphetamine. When Brennan and her team identify the deceased to be a former DJ of the dance club, Booth and Brennan investigate a rival DJ and the owner of the dance club.
Howard Epps, a death row inmate, has less than two days left before his execution. When his attorney asks for Booth's help to prove his innocence, Booth agrees to look over the case and asks Brennan and her team to help him, even though he is convinced of Epps' guilt.
Brennan's former professor and ex-lover, Michael, arrives at the Jeffersonian just as an investigation into the death of a woman found hidden in a refrigerator begins. Brennan works to gather evidence for the prosecution, only to discover Michael has been appointed expert witness for the defense.
Two days before Christmas, Booth brings in the body of a man found in a fallout shelter. While Brennan is eager to examine the body, her colleagues want to go to the company's Christmas party. When Zack cuts into the bones of the man, he accidentally releases a deadly fungus causing the team, including Booth and Dr. Goodman, to be quarantined in the lab over Christmas.
Brennan and Booth investigate the body parts of a woman found in different locations by Los Angeles International Airport. However, Brennan and her team have trouble identifying the victim when they discover she had extensive cosmetic surgery done, which altered the core architecture of her skull.
An agent from the State Department is sent to perform a security review on Brennan and her team. Meanwhile, the burnt body of a woman is found in a car with signs her child was kidnapped, leading Booth and Brennan to suspect the child's father, Carl Decker. Their investigation is complicated by their discovery that Decker is in the witness protection program.
A decomposed corpse in a superhero outfit is found in an alley. Booth and Brennan discover the victim was a fan of comic books and had engaged in role playing with his friends. His attempt at being a hero, however, had deadly consequences.