Booth and Bones inform Levi parents of his death. They tell Booth and Bones that Levi ran off to Washington with a boy named Josef. The mother tells them that they were in contact with Levi and Josef through a neighbor's phone and reported him missing when they lost contact.

Back at the Jeffersonian, Angela says that they are still looking for body parts. Cam tells Angela that Michelle has a hot boyfriend. Hodgins arrives and says that he found Kudzu on the bones which leads him to believe that it hasn't been disturbed for two months, shortly after he left home. Hodgins says that it appears that Levi was caught under a coal car.

Bones and Booth search in Levi's room and finds a rock collection under his bed. Levi's mom says she has never seen it before. Levi's mom asks to have the photo of Levi. After they hand it to her, she starts to cry.

As they leave the house, they notice a girl named Sara watching them. She asks if they are there about Levi. Her brother calls her to come to him, but Booth gives her his card before she leaves. They obtain Josef's address and head that way.

They go to his apartment and find that he is holding a party where several Amish people drink, make out and smoke weed. They take him to the institute. He says that Levi moved out a few months ago. He says that Levi had secrets. Josef explains that Levi snuck out of work. Josef says that he is going to return to his church as soon as he gets his wild out. He thought that Levi had his own plans and probably wouldn't come back to the Amish community.

The rocks are brought back to the lab and are examined by Hodgins and Sweets. Sweets arranges the rocks and finds that they make up a practice piano. He says that Levi probably felt ashamed since Amish are not supposed to play instruments. They figure that Levi was in contact with a music teacher in town.

Clark returns to the Institute dirty from his search. Bones says until they find more bones, she can't determine a cause of death. Clark says that he prefers to work in the lab. Bones tells him that he is the most qualified to be in the field.

Michelle visits Cam and asks her if she had made a decision with the dance. Cam asks Michelle if she is having sex yet. She says some people think God will smite her if she is. Michelle tells Cam that she is not her real mom then leaves.