Air date: 11/15/06

The team investigate the murder of two kidnapped teenage twin boys. The boys were placed in a spaceship-like capsule and buried alive underground. Soon, Brennan and Hodgins find themselves victims of the "Grave Digger", and Booth frantically searches for them as they slowly run out of oxygen underground.

The Headless Witch in the Woods

Air date: 11/29/06

Brennan and Booth investigate when a headless corpse is found in the woods along with a frightening video tape of events on the night of the murder. Meanwhile, Hodgins and Angela are assigned to find any possible information on the video, much to Hodgins' glee, as Angela literally jumps into his lap out of fear of what she sees. The murder suspects claim that "Maggie" killed the victim, and Brennan even finds a second, unidentified head that seems to corroborate that claim. At the end of the episode, after the killer is caught, Hodgins and Angela are relieved to turn off the video, but then they notice the silhouette of a headless female figure with an axe heading toward the victim right before he was killed. Freaked out, they both offer probably correct and rational theories explaining it, with Angela fearfully asking Hodgins at the end, "Can I come sleep over at your house?", much to Hodgins' obvious pleasure.

Judas on a Pole

Air date: 12/13/06

Zack defends his dissertation to obtain his doctorate and asks help from a colleague. Meanwhile, Booth and Brennan are called to the scene where a man's body was found gutted, burned and hung like a scarecrow on the roof of a hotel that housed Federal witnesses. Booth determines the victim was a snitch working in an organized crime syndicate. Brennan's brother, Russ, informs her of a phone call he received from their father, warning him they are both in danger. Soon after, a priest contacts Brennan telling her that her father insists she and Booth drop their case. They determine the body found was actually an ex-FBI agent, tracking Russ to kill him - hence explaining the warning from Brennan's father.

The Man in the Cell

Air date: 1/31/07

Booth and Brennan are ordered to the cell of serial killer Howard Epps to identify the remains of an inmate. To their surprise, the charred remains don't belong to Epps. It's soon learned Epps has escaped and is on a revenge path, which involves Booth's young son, Parker. Due to the danger of the case, Brennan must get FBI protection. Cam inhales a toxin while performing an autopsy, which puts her life in danger.