Its been six weeks since Booth and Brennan have seen each other. Booth has been recovering from brain surgery, and Brennan has been on a dig in Guatemala. Angelas psychic, Avalon Harmonia reveals while reading Angelas tarot cards that there are multiple bodies buried under a Washington,DC fountain. Angela shares the information with Brennan and Booth, but theyre both a little skeptical. The lead pans out, and the duo find the remains of 11 bodies exactly where the psychic said they would be. Meanwhile, Sweets has certified Booth mentally fit to return to duty after his brain surgery, but Booth is still experiencing some side effects from the coma.
Episode 2 - The Bond in the Boot
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 liquefied remains of a CIA agent in the trunk of a car. Meanwhile, Brennans new best selling book causes tension between her and Booth, and Wendell loses his scholarship.
Episode 3 - The Plain in the Prodigy
When human remains are found alongside the railroad, Brennan and Booth are called to the case. The bones belong to Levi Yoder, a member of the Amish community who disappeared two months ago, during his Rumspringa, or exploration of the outside world. Brennan and Booth discover that Levi was a piano prodigy, and their investigation leads them to believe that his extraordinary talent may have lead him to an untimely death. Meanwhile, Cam copes with the stress that comes from being a new parent.
Episode 4 - The Beautiful Day in the Neighborhood
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 Booths son attempts to find Booth a girlfriend.
Episode 5 - A Night at the Bones Museum
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. Brennans 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 Booths supervisor and former intern, and Sweets girlfriend Daisy Wick (guest star Gallo) returns to the Jeffersonian.
Episode 6 - The Tough Man in the Tender Chicken
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.
Episode 7 - The Dwarf in the Dirt
Stephen Fry returns as Dr. Gordon Wyatt. Booth, still suffering some lingering effects from his brain surgery, has to get re certified for FBI marksmanship, but is not the accurate shot he was before going under the knife. He and Brennan investigate the death of a little person who was a former wrestling star.
Episode 8 - The Foot in the Foreclosure
Booths grandfather comes to live with him and tags along as Brennan and Booth investigate human remains that were found by a real estate agent while showing a property to prospective buyers.
Episode 9 - The Gamer in the Grease
When the remains of a competitive gamer are discovered in a grease truck, Brennan and Booth are called to investigate the case. The victim, Steve Rifton, is the only active player known in the gaming community to have received a perfect score on a famous video game. Steve turned his success into a lucrative partnership with a gaming referee and charged fans to play on the very machine that gave him the perfect score. But between sour business deals and bitter competitors, the team at the Jeffersonian must work to narrow down the many suspects with motive for ending Riftons reign as gaming king. Meanwhile, Hodgins, Sweets and Jeffersonian intern Colin Fischer take turns camping out for tickets to a movie premiere.
Episode 10 - The Goop on the Girl
When a man dressed as Santa Claus blows himself up during a botched bank robbery, Brennan and Booth work to identify the bomber and determine his motives. Meanwhile, Brennan makes plans to spend Christmas in El Salvador, but her father convinces her to spend the holidays with him and Margaret Whitesell, a newly discovered distant relative.
Episode 11 - The X in the File
Brennan and Booth travel to Mexico to investigate human remains with extraterrestrial attributes Angela and intern Wendell come clean about their relationship.
Episode 12 - The Proof in the Pudding
Mr. White and his team of government agents put the Jeffersonian Lab on lock down and demand that Brennan and her forensics team determine a cause of death for an unidentified, but highly classified set of remains. As the team gets to work, their findings lead them to suspect they are investigating one of the most famous presidential assassinations in history. Meanwhile, Booths boss, Andrew Hacker, helps him break into the lab and determine the motive behind the mystery investigation, and a frustrated Cam worries that Michelle may be keeping a big secret from her.
Episode 13 - The Dentist in the Ditch
When a human skeleton is discovered in the trenches of an old Civil War battleground, Brennan and Booth are called to the case. Despite the historical location, Brennan quickly identifies the bones as belonging to Dan Pinard, a present day local dentist. While Booth investigates suspects, including the victims former boyfriend, Hodgins and lab intern Vincent Nigel Murray work doggedly to clean the bones of a stubborn clay residue which is preventing the team from determining a cause of death. Meanwhile, Booths brother, Jared, returns from his travels with some suprising news.
Episode 14 - The Devil in the Details
Brennan and Booth investigate a set of uniquely disfigured remains allegorizing biblical text. As they acquire more information about the victim, a former patient of Dr. Adam Copeland at Havenhurst Sanitarium, they are confronted with suspects who are hard to characterize as either good or evil. Meanwhile, Jeffersonian intern Arastoo Vaziri reveals a secret about his past.
Episode 15 - The Bones on the Blue Line
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.
Episode 16 - The Parts in the Sum of the Whole
When Dr. Sweets book gets published, both Booth and Brennan read it and tell him about the first time they met 6 years ago. The episode will give a new perspective on Booth and Brennans relationship, and will also give viewers the chance to see Zack Addy again, and Dr Saroyan as a New York Coroner.
Episode 17 - The Death of the Queen Bee
The teams 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 Angelas help, they identify the victim as one of Brennans 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
Episode 18 - The Predator in the Pool
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 teams 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.
Episode 19 - The Rocker in the Rinse Cycle
Booth and Brennan investigate a death at a rock n roll fantasy camp where the murder weapon is a Gibson 57 Les Paul Black Beauty.
Episode 20 - The Witch in the Wardrobe
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
Episode 21 - The Boy with the Answer
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.
Episode 22 - The Beginning in the End
The team works to uncover clues buried under a lifes worth of possessions saved by a hoarder in order to solve the mystery of his death. Meanwhile, Angelas father has a specific purpose for his most recent visit, and Brennan and Booth are confronted with unique opportunities.