Air date: 8/30/06

Brennan and Booth investigate the site of a train wreck where the bodies of a senator and a high-profile businessman are found within the wreckage. The businessman's body is found in a car on the train tracks, and at first glance, it is an apparent suicide. While investigating a possible connection between the two victims, Brennan and her team discover the businessman is still alive, but severely injured, at a local hospital, and the body at the scene is someone else. As the clues begin to unravel, the investigation gets more complicated when details of the man's private life are revealed, leading Brennan and Booth to a private detective who may hold key information. Meanwhile, Brennan is introduced to Dr. Camille Saroyan, a first-rate pathologist who has been hired as the head of forensics at the Jeffersonian, and more importantly, Brennan's boss. It doesn't take long for Brennan to figure out "Cam" is a little too familiar with Booth and they share something of a past. Also, Booth encourages Brennan to visit her mother's grave site for the first time.

The Mother and Child in the Bay

Air date: 9/6/06

Booth and Brennan investigate the remains of a woman and fetus washed up on the beach of the Delaware Bay. The body is identified as that of Carlie Richardson, a pregnant newly-wed whose mysterious disappearance one year ago had been a major national news story. However, the immediate prime suspect, Richardson's husband, has also disappeared. Meanwhile, Booth is annoyed his ex-girlfriend Rebecca, the mother of his son Parker, is letting Parker spend so much time with her new boyfriend.

The Boy in the Shroud

Air date: 9/13/06

Brennan and her team dig though the trash to find clues when a young man wrapped in a shroud is found among garbage. After Angela is able to identify the deceased boy, Cam quickly assumes the main suspect to be the boy's girlfriend, Kelly, who is a product of the foster system. Brennan is hurt by this as she is also a product of the foster system. Meanwhile, things get tense when Brennan and Cam struggle for power in their disagreement on work styles. Cam threatens to fire Brennan even if it costs her the whole Jeffersonian team.

The Blonde in the Game

Air date: 9/20/06

Skeletal remains of a young girl are found, and when brought back to the lab, the team recognizes this is not just any murder but Howard Epps, who the team encountered in the first season, a convicted serial killer on death row. He left clues leading to another body, a fresh kill only a week old. Brennan and her team scramble to decipher Epps' cryptic clues as they try in a desperate effort to find his accomplice who has been killing for Epps. When they realize another victim may be alive, the team works under pressure to try to find the young girl.