In the 100th episode, Bones looks back at the first time Booth and Brennan worked on a case together. The formation and evolution of their relationship, as well as the relationships of the other Jeffersonian workers, is examined.
Booth and Brennan examine disfigured remains that oddly relate to biblical text. They discover that the victim was a patient at a sanitarium, and have trouble sorting through the list of suspects they uncover.
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.
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 go to New Mexico to investigate when a body is found in the desert near Roswell. Meanwhile, a relationship between two people back at the lab is revealed.
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.
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.
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.
Brennan and Booth are asked to investigate the death of a man who was murdered for the secret contents of his briefcase. They suspect that secret operatives are at work, and their theory is proven correct when they find the liquified remains of a CIA agent in the trunk of a car. Meanwhile, Brennan's new best-selling book causes tension between her and Booth, and Wendell loses his scholarship.
For the past six weeks Booth has been recovering from brain surgery, and Sweets has finally certified him as mentally fit to return to duty. Meanwhile, while reading her tarot cards, Angela's psychic reveals that there are several bodies buried under a fountain. Booth and Brennan are skeptical about checking it out, but are surprised when they find the remains of eleven bodies exactly where the psychic said they'd be.
