The episode begins with a man in a parachute stuck in a tree following a sky dive. The strap snaps and he falls down some distance and gets stuck again for a while and that is when he finds himself face-to-face with a dead body in a giant cocoon. He screams. At home, Brenan encourages her baby to play peek-a-boo. Some other kid at day care can play the game and so Brenan wants Christine to be able to play it too. Sweets, joins her in the mission. Booth gets a call about their latest crime and they leave to check the “moth man” Hodgins thinks that it could be some new species.
Sadly, no, it is a human being; a Caucasian male. Nearby is a wrecked car. Booth quickly determines that somebody pushed the bar, which hit a boulder, which catapulted the victim into the trees above. Brenan cuts a small hole in the cocoon, unleashing a shower of bugs. They land of Bones' face, but she isn't at all bothered, of course. Hodgins pockets one of them and brushes off the rest from her face. Back at the lab, Cam tells Hodgins that the wrecked car belonged to a man named James Sutton. Hodgins knows him; Sutton is an archaeologist and a book writer. He has written the Temple of Doom. The victim has chronic sinusitis. Hodgins estimates that the body was cocooned by the very worms that fell on Brenan. Sweets, tells Booth that Sutton wrote these conspiracy books and sold bogus artifacts based on the books.
They then talk to the wife, Marina. She is a Russian and she is with her brother, who is now also her translator. She tells them that her husband used to bring all sorts of thing; he hands over a key to a storage facility. Marina, who is pregnant, is sad and weeping and her brother comforts her. Booth and Brenan head to the victim's storage facility. They realize that Sutton almost worked there. There are a lot of documents around and also there are bones! Brenan tells Booth that these bones are around 25,000 years old. Back at the lab, Clark tells them that the remains were found near a lake in Chechnya. Looks like Sutton wasn’t a sham after all. Looking at the notes, Clark is sure that Sutton knew about the importance of the bones.
Clark takes the bones to his new office in the anthropology department. But Brenan wants to examine the bones and Cam reminds her that she has a murder to solve. Brenan is unhappy and she reminds Clark that she is the one who taught him. He says that he is thankful. He leaves and Brenan indirectly tells Cam that she might not be available incase Clark needs help. Booth points out this pattern of competitive behavior to Brenan and she does not take it particularly well. They then head to Sutton’s publisher, who explains that he recently called and said he had found something of real scientific relevance. They spoke a month ago and he was supposed to meet her seven days back. The estimated TOD is six days.
The publisher then explains that the author sold all of his phony artifacts to the same person; a businessman in Texas. Sweets, tracks the sales to a fundamentalist, Wilson, who funded Sutton’s most recent trip to Russia. Booth wonders as to why would a fundamentalist buy artifacts from Sutton when he did not even believe in its existence! Booth asks Sweets to talk to Wilson. Back at the Jeffersonian, Brenan visits Clark, who explains that the bones indicate that Homo sapiens and Neanderthals were living together in the same cave using the same resources. Brenan is intriguied. She then notices that some of the remains indicate a spear wound. That is a crime (despite it being thousands of years ago) and so now the bones are hers.
Clark is stunned. They then go to Cam with their issue. Cam is in a dilemma and comes up with a brilliant idea; she tells that Clark can keep the bones but Brenan too will have access to it. "Drop the egos and figure out what happened to this poor caveman," she says. This time, Brenan is shocked. Sweets, questions the Texas businessman, Wilson, who believes that the Earth is 6,000 years old, according to the book of Genesis. Sweets, tells him that according to the scientists the Earth is 13 billion years old. Wilson scoffs. Sweets, then points out that despite his belief, Wilson also bought a number of artifacts that were reportedly far older. "Do you destroy the artifacts that contradict your creationist views?" Sweets, asks.
Wilson admits; in a way. So Sweets theorizes that Sutton actually found something of real value, the old bones and refused to hand them over to the man who funded his trip (probably because Sutton knew that Wilson destroyed the artifacts). Wilson insists that Sutton stole from him. Wilson stops talking and lawyers up. Meanwhile, Clark makes another shocking discovery; the Neanderthal and the homo sapien mated and so they had a child that was half Neanderthal! This is big (but not as much for Angie who doesn’t really understand the significance).
Brenan then examines marks on the more recent victim's body and theorizes that, months before his death, the dead man was flogged with a leather whip. Hodgins isolates the isotopes and finds out that the hide can from the Chechen Republic. So Sweets interviews Marina again. She admits that her very traditional family was horrified when they learned she was pregnant with a foreigner's baby. Marina's father flogged Sutton. Sweets, wants to know if her father then followed the couple to America. Marina says that he did not; but her family disowned her. Back at the lab, Brenan congratulates her former pupil on his great discovery. She admits that she was busy competing and failed to notice something so remarkable.
Brenan then turns her attention to solving the 21st century murder. She discovers that a major artery was severed, causing the victim to lose consciousness in 30 seconds; Sutton died of exsanguination! Finally they have their COD. So, someone must have enough training to deliver such a heavy blow. They then find out that Marina's brother was Special Forces back in Russia. Nowadays, he bets on the horses. Booth states that the brother was broke two weeks ago and then he had $20,000 transferred to his account! Booth theorizes that the father paid the son to kill Sutton and regain the family name. Marina's brother goes silent. He will say no more.
Brenan looks again at the wound and notices that the sharpness of the cuts on the victim are consistent with a bookend. So Booth and Brenan head back to the publisher's office, and discover traces of blood on the floor. The publisher admits that she lost her cool when Sutton left her out of it and insisted on publishing in a legitimate scientific journal. So she killed him in a fit of rage. Case Closed. Later, Brenan allows Clark to have his moment and reveal the historic finding. Booth is pleasantly surprised. Well, Clark puts it up in the form of an act where this particular family was an outcast.
The parents were attacked by a homo sapien and were killed. The attacker also died in the fight. The little child who was three years old, did not survive as no one in the village wanted her; she was half Neanderthal! The little kid starved to death. Actually, the father crawled towards the mother before dying and hugged her as they died.
The child too crawled up to them and lay next to her parents and she died few days later. This is how Sutton found the bones; the three of them together! At home, Booth is pleased with Brenan’s actions. She tells him that she does not want to pass on her failings to Christine. She wants Booth to work on it as well. Well, what failings? The episode ends.