
Dr. Temperance Brennan, a forensic anthropologist who works at the Jeffersonian Institution and also writes books, has an impressive ability to read clues from victims' bones. Consequently, law enforcement calls her to assist with investigations when remains are so badly decomposed, burned or destroyed that standard identification methods are useless. Brennan is teamed with Special Agent Seeley Booth, a former Army sniper, who mistrusts science and scientists when it comes to solving crimes but who has developed respect for Brennan, both professionally and personally.
A man who wanted to talk to Booth about a possible government cover-up is killed before their meeting takes place; as Booth and the team investigate the conspiracy surrounding the man's death, Booth's future with the FBI becomes uncertain.
As Brennan and the team try to absolve Booth and get him out of prison, the remains of a man who has been dead for 16 years prove to be significant; Booth encounters criminals he was responsible for incarcerating.
The team works with Special Agent Aubrey to investigate a far-reaching conspiracy in the government; DNA found on a previous victim linked to the scandal helps the narrow down the suspect pool.
With intern Rodolfo's help, the team investigates the murder of a conservative radio host whose remains were found in a storm drain; Special Agent Aubrey endeavors to gain Booth's trust; Brennan worries about Booth's mental health.