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 Cam’s stepdaughter, Michelle, in line.
Songs: The Drawbacks -- Complicated, Great Lake Swimmers -- River's Edge
Brennan and Booth are called to investigate when human remains are found during a neighborhood block party. With numerous hidden secrets and scandals, each neighbor in the cul-de-sac has a motive for the murder, leaving Booth, Brennan, and Sweets to look through the drama to find their suspect. Meanwhile, intern Arastoo admits the truth about his past.
The Rising Tide -- Liliko'i Lover, Frank Sinatra
-- The Good Life
Brennan and Booth investigate when charred human remains are found on an electrical fence. The corpse is determined to be a mummified Egyptian royal on loan to the Jeffersonian exhibit, and when the exhibit curator is murdered, the team must look to their own to find the killer. Meanwhile, Brennan goes on a date with Booth's supervisor, and Sweets' girlfriend returns to the Jeffersonian.
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.
Songs: A.A. Bondy -- When the Devil's Loose
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.
Songs: Glass Pear -- My Ghost, Skybombers -- Reason to Live
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 link a partnership with a gaming referee, but this partnership created animosity toward him in the gaming world. Meanwhile, Hogins, Sweets and intern Colin Fischer camp out for tickets to a movie premiere.
Matthew Perryman Jones -- Rain or Shine, Matthew Ryan
-- The World Is...
When Max, Brennan's father, gets in contact with Margaret Whitesell, he asks her to spend Christmas with him and Brennan. Meanwhile, Booth and Brennan investigate a bank robbery gone wrong in which a man dressed as Santa Claus was blown up.
Songs: Bob Dylan
-- Here Comes Santa Claus, Johnny Reno -- O Christmas Tree, Ingrid Michaelson
-- Snowfall, Matt Alber -- Star of Wonder
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.
Songs: The Bird And The Bee -- What's In The Middle
Brennan and Booth are called to investigate when a set of remains found in a church appear to be demonic. 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
As Sweets is finishing up his book on Booth and Brennan they tell him how they first met several years ago.
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.