Episode 31 of "Bones"
s02e09 Aliens in a Spaceship

When the bodies of twin teenage boys kidnapped five years earlier are discovered in Pennsylvania, Booth and Brennan find themselves on the trail of the Grave Digger, a notorious serial killer whose M.O. is to kidnap, bury his victims alive and make a single, exorbitant ransom request. If the money is not paid in the specified period of time, there is no further communication and the victims are left to die. During the investigation, Brennan and her scientist colleague Dr. Hodgins become the Grave Digger's latest victims, forced to try to solve their own kidnapping from an underground grave.