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 Angela tells them about it. However, when the lead pans out, Booth and Brennan find 11 bodies buried underneath a fountain. Meanwhile, Booth has to deal with side effects of his coma and brain surgery.

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 Booth question the CIA’s Assistant Director of Intelligence, they question the man’s allegiance to the U.S. Meanwhile, the financial success of Brennan’s latest book leads to a rift between her and Booth; and when Wendell loses his scholarship, the team searches for alternate funding in order to keep their intern around.

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 may have lead to his death. Meanwhile, Cam tries to cope with the stress of being a new parent, while Booth does his part to keep Cama 's stepdaughter, Michelle, in line.

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 a girlfriend.

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, the team suspects foul play. Brennan, 's investigation of the curator sheds new light on the life of the Egyptian royal, turning their case into one of historic proportions. Meanwhile, Brennan goes on a date with Booth, 's supervisor and former intern, and Sweets, ' girlfriend Daisy Wick returns to the Jeffersonian

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...

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 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.

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

Brennan and Booth investigate the motive of a failed bank robbery that ended with a man dressed as Santa Claus blowing himself up. Meanwhile, Brennan’s father tries to persuade her to spend the holidays with him and a distant relative (Zooey Deschanel) rather than return to Central America

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. '

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. '

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. '

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. '

When a subway train is thrown off the track by 60,000 gallons of flood water, a partially skeletonized body emerges out of the overflow. While Dr. Sweets, a passenger on the derailed train, copes with post traumatic stress, the rest of the team and intern Daisy Wick get to work on identifying the victim as Martin Aragon, a professional ghost writer caught up in a deadly love triangle. Meanwhile, Brennan releases her second book to great success, but has to accommodate a nosy reporter, and Sweets' near-death experience leads him to make a drastic decision

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.

The team's latest case takes Brennan back to her alma mater, Burtonsville High School, where she and Booth investigate the discovery of an unidentified skull and upper torso. With Angela's help, they identify the victim as one of Brennan's classmates, and notice a possible connection to a second murder committed 15 years prior. Brennan and Booth go undercover as a married couple at her class reunion to interrogate a set of suspects, where even as an adult, Brennan is still predictably misunderstood and her only friend lies in a strangely dark and offbeat janitor.Meanwhile, Hodgins spills a lab secret.

When human remains are discovered in the belly of a shark, Brennan and Booth are brought in to identify the missing person. Evidence suggesting the victim had been the prey of several fish directs the team's investigation to The Aquarium of the Atlantic, where a guest lecturer and notorious self-help guru preaching the healing power of the ocean has gone missing. Meanwhile, both Brennan and Booth navigate their own relationship when a marine biologist shows interest in Booth

When the body of a rich adventure-seeker is found in a hotel laundry machine, Booth and Brennan are led to the last place he was seen: a Rock 'n Roll Fantasy Camp. While Brennan and Booth lead the investigation outside the lab, Hodgins, Angela and intern Arastoo use a fragment of prehistoric wooly mammoth tusk - found with the remains - and Angela's knowledge of the music industry to connect the evidence to potential suspects. Meanwhile, Cam looks for a doctor for her daughter Michelle

A cabin burns down in the woods revealing two bodies, one of a modern-day witch and one from the days of the Salem Witch Trials leading Booth and Brennan into the world of Wicca to find a killer. Meanwhile, when Hodgins' reckless driving gets him and Angela arrested and thrown in jail, Sweets and intern Clark Edison step into unfamiliar territory to help out the team

The trial of The Gravedigger hits close to home for members of the team, and everyone at the Jeffersonian must work overtime to uncover the forensic evidence to elicit a conviction

The team works to uncover clues buried under a life's worth of possessions saved by a hoarder in order to solve the mystery of his death. Meanwhile, Angela's father has a specific purpose for his most recent visit, and Brennan and Booth are confronted with unique opportunities.