Brennan examines a human mandible nestled amongst the train tracks in Virginia. It appears that the victim was dead before being dumped on the tracks. The remains were then dragged, and the corpse broke apart as it smashed against the rails. Bones could be scattered for miles. Booth must divert all trains so they can search for the rest of the body. Later, several FBI Techs join Booth and Brennan on the tracks. Brennan is glad to see Booth wearing his "Cocky" belt buckle again. She likes it because it's "Boothy," though Booth himself isn't sure why he owns such a thing. Brennan examines a femur with a bone cyst. The cyst resulted from a parasite not often found in the United States. She also locates a pelvis and a tibia. The victim was a teenage male.

Michelle asks Cam if she and her boyfriend Perry can stay out all night after their high-school dance. Cam says she'll think about it. Perry pulls up in his car to pick up Michelle. Cam waves goodbye, but is troubled when she glances back and sees them making out passionately. At the lab, Clark believes the victim was beaten based on perimortem fractures. Angela notes that the clothing scraps found on the scene look hand-stitched. Was the victim from another country? Cam arrives and asks, "When do teenagers start having sex?" Angela guesses this is about Michelle. Clark hurries off to supervise in the field and avoid this conversation. Brennan is baffled. According to her isotope analysis, the victim grew up in the United States. Yet she can find no evidence of pesticides, processed foods, or contact with electricity. It's as though he grew up in the 1800s but died two months ago. Later, as Cam reads a book entitled Talking to Your Teen about Sex, Brennan bursts in with the solution: their victim is Amish.

The victim is Levi Yoder, whose parents reported him missing two months ago. Levi has a DMV photograph, so he must have been on his rumspringa. Brennan explains that a rumspringa is "a period when Amish youth are encouraged to explore the outside world." Afterward, nearly 85% of them return home. Levi's parents, Daniel and Rebecca Yoder, are devastated. Levi went to Washington with Josef Beachy, another Amish boy. He called weekly to check in via a neighbor's phone. When Levi stopped calling, Rebecca contacted the Beachys. She discovered that Levi and Josef were no longer rooming together. The track on which the body was found is used by southbound trains. The body likely came from the north. However, the tracks branch out into dozens of other lines, so they still have plenty of searching to do. Angela asks about Michelle. Are she and Perry having sex? Hodgins interrupts: There is carbon, nitrogen, oxygen, and sulfur on the bones. The victim was hooked beneath a coal car.

At the Yoder Residence, Booth and Brennan search Levi's room. Under the bed Booth finds a wooden box filled with stones. There are blue feathers glued to the top of the box. Rebecca asks Booth for the photograph of her son. She weeps, cradling her son's image. Outside, Booth and Brennan encounter an Amish girl, Sarah. She asks about Levi, but her brother calls her away. Booth slips the girl his card before she heads off. Booth knocks on the door of an apartment. Josef Beachy answers, a bong in hand. Inside, a wild party rages with Amish guests. Booth tells Josef that he is coming with them. Brennan gets the last word: "This is not in the proper spirit of rumspringa!" At the FBI, Josef explains that Levi moved out because of the parties. They didn't keep in touch. Josef remembers that Levi would disappear for hours at a time, and says he suspected that Levi didn't plan to return to Amish life.

Sweets examines the rocks from Levi's room, which Hodgins found nothing unusual about, and realizes that they're a practice piano. There are 52 light rocks and 36 dark rocks, just like the keys of a piano. The songbird feathers are further signifiers of music. Levi kept them hidden because the Amish are not supposed to play instruments. Levi had a job in town; perhaps someone there taught him to play. Brennan believes that the body was face up when an exposed gear-lever hooked the sternum. She hasn't found cause of death yet, so she wants Clark back in the field. They need the rest of the bones. Michelle asks Cam if she's decided about staying out the night of the dance. Cam asks Michelle outright if she is having sex. Michelle, angered, says she doesn't think this is any of Cam's business. Cam is not her mother. She storms out.

Booth speaks to Eleanor Turner. Levi worked for her husband, and she gave him free piano lessons. She says he was a prodigy, and suggested he explore music on his rumspringa. They kept in touch for a while. The last thing Levi sent her was a DVD. His friends were helping him audition for the National Conservatory. Later, Angela uses the DVD footage to locate Levi's apartment. The images outside the windows are not enough… until she hears something on the recording: a train. The apartment is next to the tracks. Angela takes into account the architecture, and is able to pinpoint the location of building. Karen Lin and Tony Salina, who were both on the DVD with Levi, are questioned. Karen explains that Levi moved in with them. They met at the Conservatory and "adopted" him. Karen gave him a gold medal she'd won as a kid. It wasn't real, but it was his good luck charm. They had no idea he was dead. Karen thought Levi had gone home. Days before his audition, she saw an Amish man walking into their building. She assumed it was Levi's father.

Booth and Brennan pay a visit to Daniel Yoder. Daniel is upset at the accusation that he might hurt his son. Rebecca says that Daniel has not left the farm in years. Brennan tells them about Levi's audition. They are stunned to learn that their son was a musician, and had secretly been taking lessons for years. Brennan tells Booth that Cam thinks Michelle may be sexually active. Brennan lost her virginity when she was 22, though she advised Cam to tell Michelle that seventeen and a half was a good age. Booth was having sex when he was 16, but he doesn't believe Michelle should be. Brennan accuses him of having a double standard. Booth agrees that there is, and thinks that there should be.

Sarah, the young Amish girl who lives near the Yoders, tells Booth and Brennan that she and Levi were in love. She knew that he was pursuing music, and began to worry that he might not return to the community. She shared her fears with her brother, Amos. Later, Amos left for the day on business. When he returned, he told her that Levi might never come home again. At the lab Clark, Angela, and Hodgins explain the cause of death to Cam. Karen Lin's apartment is on the fourth floor. Underneath her balcony, there is a dumpster. Hodgins swabbed the injuries to the skull, and found a powder coating used on dumpsters. FBI Techs found a dent on the dumpster, as well as dried blood: Levi's.

Amos is questioned, and he explains that Levi was going to abandon his sister. He went to Levi's apartment to make him come home. Levi tried to explain about his music, but Amos didn't understand. So Levi played for him. Amos had never heard anything so beautiful. He agreed to care for Sarah so Levi could pursue his gift. Michelle apologizes to Cam. She knows that Cam was looking out for her. Michelle shares that she and Perry haven't slept together. Perry wants to, but Michelle isn't sure if she does. Is that weird? Cam assures her that it's okay to wait.

Clark reassembles the bones found in the wheels of the train. He recovered fragments from the left arm, left hand, and right foot. Brennan notes there are fractures on the hand that occurred prior to death. Angela believes the lid of a keyboard caused the injuries. There was only one spot open at the Conservatory. Tony was already in, but Karen was auditioning. She could have injured Levi to stop his audition, and then killed him when he wouldn't back down. At the lab, Booth finds Perry waiting for Michelle. He makes sure that Perry knows he is a trained sniper, and that Michelle deserves respect. Perry hears him loud and clear.

Karen is questioned, and she says that she wasn't competing with Levi. Her grandfather worked at the Conservatory. She didn't have to audition. Karen has no knowledge of Levi's injury. The last time she went to her apartment, Levi's things were there, but Levi and his money were gone. FBI techs find a keyboard at the Conservatory with dried blood on the lid. They also found fingerprints: Levi's. Why would Levi injure himself? Booth believes he was planning on returning to the community. He wanted to ensure he couldn't change his mind. Booth realizes that they never recovered Levi's money or the medal from Karen. Was this all about the money?

Booth leads a young thief into the FBI. Residents of Karen Lin's building reported items missing around the time Levi died. They tracked down the robber and arrested him in Baltimore. He makes a full confession. Levi was struggling to hang on to the medal from Karen when he fell over the balcony. At the Yoder Residence, Booth and Brennan tell Daniel and Rebecca that their son planned to return home. Brennan says they have something for the Yoders, and takes out a portable DVD player. Daniel says that they can't accept that, but Brennan opens the case and plays the DVD. It's a video of Levi playing the piano. The music is beautiful, and the Yoders are deeply moved.