Brennan and Booth are called to investigate when a set of remains are found that reference a biblical text. As they dig into information about the victim, who is a former patient of Dr. Adam Copeland at Havenhurst Sanitarium, they encounter unique suspects who they have a hard time deciding whether they are good or evil. Meanwhile, intern Arastoo Vaziri talks about a secret from his past.
A skeleton is discovered at a Civil War battleground, and Brennan and Booth are called to investigate the case. Despite the location, Brennan finds that the remains belong to Dan Pinard, a local dentist. While Booth looks into a list of suspects, Vincent the intern works to clean the bones of clay residue. Meanwhile, Booth's brother returns with surprising news.
Mr. White and government agents demand that Brennan and her team look into the cause of death for a set of remains and closes the Jeffersonian Lab to do so. However, the team soon find that they are investigating an infamous presidential assassination. Meanwhile, Booth's boss, Andrew Hacker, helps Booth break into the lab to determine the motive behind the investigation.
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 a relationship.
Booth and Brennan investigate the case of a man in a Santa Claus costume who tried to rob a bank but was blown up in the process. Meanwhile, Brennan's father Max asks Margaret, a distant relative of Brennan's, to spend Christmas with him and Brennan.
Booth and Brennan are called in to investigate the death of a competitive gamer. The gamer's success gave him many admirers -- but also a lot of enemies, which make for multiple suspects in the case. Meanwhile, Fisher bonds with Hodgins and Sweets.
A real estate agent discovers human remains while showing a property, and the team is called in to investigate. Meanwhile, Booth's grandfather moves in with Booth, and tags along with him while he's working the case.
Booth and Brennan delve into the murder of a dwarf who used to be a wrestling star. Meanwhile, Booth discovers that he's not as good of a marksman as he was before his surgery, and has trouble getting re-certified at the FBI. Dr. Gordon Wyatt also returns.
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.
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.