Pilot episode. 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.
When the decaying corpse of the Venezuelan Ambassador's son is found hanging from a tree on the campus of an exclusive private school, a simple suicide case quickly turns into a web of lies, sex and scandal involving the school's staff and students.
When Brennan and Angela get caught in a fight in a dance club, Brennan kicks someone into a wall, which causes the wall to break open and reveal a mummified corpse and a meth stash.
A death row inmate asks for Booth's help to prove his innocence before he is scheduled to be executed. Booth agrees and asks Brennan and her team to help him out.
Brennan is about to go out for dinner with her old professor and ex-lover when Booth asks her and her team to help identify the remains of a young woman found in a refrigerator.
Brennan and her team are brought in to identify the body of a man found in a fallout shelter. While cutting into the bones of the man, Zach accidentally releases a deadly fungus, causing the team to be quarantined over Christmas.
Brennan and Booth investigate the body parts of a woman found near L.A. International Airport. Their investigation is slowed due to extensive cosmetic surgery the victim had done.
When a woman’s burned body is found in a car with signs that her child was kidnapped, Brennan and Booth suspect the father, Carl Decker. But things get complicated when Decker turns out to be in the Witness Protection program.
Brennan and Booth investigate the origins of a decomposed body that's been found in a local alley and determine it's the remains of a shy teen with an alter ego.
Booth and Brennan investigate when a dug up corpse is found in the back of a gang member's car. While being questioned, a drive-by shooting allows him to escape. Booth and Brennan follow the clues, which lead them to an empty grave and another body in a grave at a wealthy senator's house, where the gang member used to work.
Brennan and Zach investigate a small jet crash that was carrying some Chinese diplomats and a woman. At the crash site, Brennan finds some bone fragments that do not belong to any of the passengers, but might belong to a man who has been missing for five years. Although ordered to work only on the diplomats, Brennan and her team go rogue to try to discover the identity of the extra bones.
When Brennan decides to give online dating a try, she ends up the target of a shooting at the local restaurant where she's meeting her date. The resulting investigation reveals that the shooter could be connected to either of the two cases she's currently working on.
Brennan and Booth stumble upon a subterranean world of homeless people when they find the remains of a filmmaker in the ventilation shaft of an underground tunnel.
While on vacation, Angela's boyfriend goes missing . When a skull shows up, she asks Brennan for help in identification, concerned it might be her boyfriend or the female guide who went missing with him. The investigation leads the team to a violent boyfriend, the local sheriff and ultimately to a counterfeiting ring setup in the desert.
The team helps Deputy Director Sam Cullen's daughter, Amy, when she contracts a rare form of lung cancer after receiving a bone graft. Booth and Brennan learn she is not the only victim with this rare form of cancer.
Brennan receives some bones to identify, but is stunned when she discovers that the remains are those of her mother who disappeared when she was 15 years old. The determined date of her mother's death leaves Bones confused and angry.