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.

Booth and Brennan are called in when a skeleton is found in the trenches of a Civil War battleground. Brennan determines that the remains are those of a present-day dentist, but a residue stuck on the bones is keeping the cause of death from being determined. Meanwhile, Booth’s brother Jared returns with interesting news.

Six weeks have passed since Booth and Brennan have seen each other. During this time, Booth has been recovering from brain surgery and Brennan has been busy on a dig in Guatemala. Angela’s psychic, Avalon Harmonia, reveals that there are bodies buried under a fountain in DC, but both Booth and Brennan are skeptical when [...]

Brennan and Booth look into the death of a man murdered for the contents of his briefcase. The evidence leads them to suspect that a group of secret operatives were behind the murder, and their suspicions are confirmed when remains of a CIA agent are found in the trunk of a car. When Brennan and [...]

When human remains are discovered by the railroad tracks, Brennan and Booth are called to investigate. They learn the remains belong to Levi Yoder, a member of the Amish community who went missing two months before his Rumspringa. Brennan and Booth discover that Levi was a piano prodigy, and are led to believe his talent [...]

Brennan and Booth investigate human remains found at a neighborhood block party. Suburban politics and secret scandals give each neighbor in the cul-de-sac a motive, leaving Brennan, Booth and Sweets to sift through the drama to find their suspect. Meanwhile, Jeffersonian intern Arastoo comes clean about his background, and Booth’s son attempts to find Booth [...]

Brennan and Booth are called to investigate what appears to be charred human remains on an electrical fence. The mysterious corpse is later determined to be a mummified Egyptian royal on loan to the Jeffersonian. The anthropological mystery has Brennan in a tizzy, and when the Jeffersonian curator prepping the mummy for exhibition is murdered, [...]

When the remains of a chicken farmer are found on a river bank, Booth and Brennan are called to investigate. They soon uncover that the farmer, who was also a well-known animal rights activist, was about to inherit a chicken factory, leading him to make several enemies with motive to kill him.

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.

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.

The remains of a video gamer are found in a grease truck, and Booth and Brennan soon uncover that the victim, Steve Rifton, is the only gamer to have a perfect score on a particular video game. His perfect score helped him to ink a partnership with a gaming referee, but this partnership created animosity [...]

Brennan and Booth head to New Mexico to look into a case in which human remains with extraterrestrial attributes were found. There they find that their victim was a UFO fanatic known for her extensive search for alien life and her “evidence” has even Brennan rethinking human existence. Meanwhile, Angela and Wendell admit to having [...]