Air date: 2/15/06

Brennan joins Booth in his investigation regarding a dug-up corpse found in the back of a gang member's car. When Brennan and her team examine the original burial site of the corpse, they find another empty grave, leading Booth to believe that there was a double homicide.

The Man on the Fairway

Air date: 3/8/06

Brennan and Zack investigate a small jet crash that was carrying some Chinese diplomats and an unidentified female guest. 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.

Two Bodies in the Lab

Air date: 3/15/06

Two cases are brought to the Jeffersonian Institute; one concerning the human remains of whom the FBI thinks is mob boss James Cuguni, while the other concerns a possible murder victim of serial killer Kevin Hollings. When Brennan narrowly misses being the target of a shooting while waiting for a date, it becomes probable that the shooter is connected to one of these cases.

The Woman in the Tunnel

Air date: 3/22/06

The body of a documentary film-maker is found at the bottom of a tunnel shaft beneath Washington, D.C. Brennan and Booth are introduced to an underground society, whose leader thinks he might be responsible for the victim's death.

The Skull in the Desert

Air date: 3/29/06

When Angela finds a skull in the desert on her vacation, she asks Brennan for help identifying the skull as she fears that it may be her missing boyfriend's.

The Man with the Bone

Air date: 4/5/06

Booth brings Brennan to examine a 300-year-old finger bone that was found with a corpse in a national park. When they discover that the bone may have belonged to a pirate, the team is led on a hunt for pirate treasure.