When a human skeleton is discovered in the trenches of an old Civil War battleground, Brennan and Booth are called to the case. Despite the historical location, Brennan quickly identifies the bones as belonging to Dan Pinard, a present-day local dentist. While Booth investigates suspects, including the victim’s former boyfriend, Hodgins and lab intern Vincent Nigel-Murray work doggedly to clean the bones of a stubborn clay residue which is preventing the team from determining a cause of death. Meanwhile, Booth’s brother, Jared, returns from his travels with some suprising news.
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The Jeffersonian team is put on lockdown by a group of government agents, who insists that they determine the cause of death of a top-secret, unidentified corpse. Booth meanwhile breaks into the lab, with the help of his boss, to figure out what exactly is going on with the secret investigation.
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Brennan and Booth travel to Mexico to investigate human remains with extraterrestrial attributes; Angela and intern Wendell come clean about their relationship.
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Brennan and Booth investigate the death of a competitive gamer whose success and business partnerships earned him plenty of admirers—but also lots of enemies. Meanwhile, Hodgins, Sweets and intern Colin Fisher camp out for movie tickets ahead of its premiere
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When a real estate agent uncovers human remains during a property showing, Booth and Brennan are called to investigate. Meanwhile, Booth’s grandfather moves in with Booth and insists on tagging along during the investigation.
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Booth and Brennan look into the murder of a dwarf who was once a wrestling star. Meanwhile, Booth, still dealing with the effects of his surgery, has trouble getting re-certified with the FBI to carry a weapon.
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Remains of a chicken farmer are found on the bank of a nearby river, and Booth and Brennan are called in to investigate. The farmer, who was an animal right activist, was about to inherit a chicken factory and had many enemies with motive to kill him — leaving the team with a lot of murder suspects to sort through.
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Brennan and Booth investigate human remains that have been charred on an electric fence. Brennan later realizes that the corpse is actually a mummified Egyptian that has been loaned to the Jeffersonian for an upcoming exhibit. When the Jeffersonian curator who was prepping the mummy for the exhibit is found murdered, Booth and Brennan suspect foul play. Meanwhile, Brennan goes on a date with Booth’s former supervisor, and Sweet’s girlfriend Daisy returns.

When human remains are found at the site of a block party, Brennan and Booth are called in to investigate. Sweets is called in for help when the politics and scandals of the neighbors link everyone with some type of motive. Meanwhile, Booth’s son Parker tries to find him a girlfriend.

The bones of Levi Yoder, a member of an Amish community, are found near a railroad. When Booth and Brennan discover that Yoder was a brilliant pianist, they believe his talent may have lead to his death. Meanwhile, Cam has a hard time coping with becoming a new parent, and asks Booth to help keep Michelle in line.