The "Bones" episode "The Archaeologist in the Cocoon" opens with a skydiver who is calling his wife from a tree. After jumping, his parachute gets tangled in the branches. While up there, he sees a dead body wrapped in a cocoon and freaks out.
Back at their house, Bones, Brennan, and Sweets are trying to get baby Christine to play peekaboo with them. They are called to the woods to see the body, where Hodgins is convinced that Mothman killed this victim. When Brennan cuts into the cocoon wrapping, a pile of worms falls onto her upturned face.
The cocoon was built up over five days by a colony of "web worms." To quickly clean the body of worms, Hodgins sets a murder of crows on the corpse to get rid of the nasty bugs.
Below, the team finds evidence of a car accident that might have catapulted the body up into the trees. But Booth notices that the gear shift is in neutral, indicating that the "accident" was staged, and this was murder. Cam confirms this by cutting into the car's seats: While wiped clean on top, the stuffing underneath is saturated with blood.
Back at the lab, Cam tells Hodgins that the crashed Jeep at the scene belonged to James Sutton, an archeologist and novel writer. Sutton was also known for selling bogus artifacts. Booth questions Sutton's wife, Marina, and her brother, Artur. Marina gives Booth a key to a storage facility where she says Sutton was storing artifacts he had brought back from a recent trip to Russia.
At the storage center, Booth and Brennan find old bones. Based on documents in the unit, Brennan believes that the bones are thousands of years old, dating back to the Paleolithic era. Back at the Jeffersonian, Clark tells Cam and Brennan that the remains came from Lake Kezanoi in Chechnya.
Booth and Brennan talk to Sutton's publisher, Diana Malkin. Diana tells B&B that Sutton believed he was finally going to be able to publish a major scientific find, based on the bones he found. Malkin also tells B&B that most of Sutton's artifacts got sold to a man in Texas named Wayne Wilson. Oddly, Wilson runs a creationist museum, which puzzles Sweets. Why would a creationist be so interested in such remains? Under questioning from Sweets, Wilson clams up and says he wants a lawyer.
Back at the lab, the team examines the bones from the storage locker. Dr. Brennan is shocked: This is the first case of both species living together at the same site. The bones include finger bones from a Homo sapiens, as well as the ribs and femur of a male Neanderthal. There are also the bones of a child of about three years old. Brennan notices an injury on one bone that indicates that these Paleolithic people were murdered. Angela and Clark later realize that the child is half Neanderthal and half Homo sapiens, and the team theorizes that the family was murdered because of interspecies mating taboos.
In taking a second look at the body, the team finds that Sutton was badly beaten up shortly before his death. Sweets talks to Marina Sutton, who explains that her traditional family beat her husband because he was a foreigner who had impregnated their daughter. The beating was so severe, it was amazing he survived at all.
Booth looks into Artur, Marina's brother. He was nearly broke until a few weeks ago, when he received a large deposit into his bank account. Booth thinks that Artur may have been paid to kill his sister's husband, but Artur clams up. However, Brennan gets a flash of inspiration about how the murder really went down. Diana Malkin killed Sutton because he no longer wanted to work with her, since he had a proper archeological find that would legitimize him. The murder weapon was a bookend from Diana's house. Booth puts her in handcuffs and takes her away.