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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. Twelve human skeletons are found, and Booth and Bones' investigation leads them to the Harbingers of a New Day, a group that wants to live in an underwater utopia. Cyndi Lauper guest stars in this episode as Avalon Harmonia.
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Brennan and Booth investigate the body of a man murdered for the undisclosed contents of a briefcase. Early evidence leads the team to suspect secret operatives are at work, and their theories are supported when the liquefied remains of a CIA agent are discovered in the trunk of a car. When Brennan and Booth interrogate the CIA’s Assistant Director of Intelligence, they are left unsure of his allegiance to the U.S. Meanwhile, Brennan’s best-selling book leads to financial success and serves as a point of contention with Booth, and Jeffersonian intern Wendell (guest star Michael Grant Terry) loses his scholarship, leaving the team to look for alternative funding to keep him around.
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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 led to his death. Meanwhile, Cam has a hard time coping with becoming a new parent, and asks Booth to help keep Michelle in line
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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.
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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 Sweets' girlfriend Daisy returns.
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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 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. Meanwhile, chemistry develops between Angela and Wendell.
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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, who is now a chef, also returns. Booth admits to Dr. Wyatt that he's in love with Brennan.
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Booth's grandfather Hank (guest star Ralph Waite) comes to live with him and tags along as Brennan and Booth investigate ashes and charred remains found by a real estate agent while showing a property to prospective buyers. The team identifies the victims as plus-size lovers, neither of whom seemed to have many enemies. Meanwhile, Hank tries to play matchmaker for Booth and lets Brennan in on some family secrets.
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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 Rifton's reign as gaming king. Meanwhile, Hodgins, Sweets and Jeffersonian intern Colin Fischer (guest star Joel David Moore) take turns camping out for the premiere of Avatar (in which Moore also played a major role).
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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 (guest star Ryan O'Neal) convinces her to spend the holidays with him and Margaret Whitesell (guest star Zooey Deschanel), a newly discovered distant relative.>
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An out-of-this-world case brings Brennan and Booth to New Mexico where they investigate human remains with extraterrestrial attributes. The victim is identified as a local UFO fanatic, known around town for her relentless search for alien life forms and whose latest "evidence" leads even Brennan and Booth to re-think outside existence. Meanwhile, a local sheriff refuses to release the bones, forcing the team at the Jeffersonian to work via satellite, and Angela and Jeffersonian intern Wendell (guest star Michael Grant Terry) come clean about their relationship.
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Mr. White (guest star Richard T. Jones) 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, Booth's boss, Andrew Hacker (guest star Diedrich Bader), 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.
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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 victim's former boyfriend, Hodgins and lab intern Vincent Nigel-Murray (guest star Ryan Cartwright) work doggedly to clean the bones of a stubborn clay residue which is preventing the team from determining a cause of death. Meanwhile, Booth's brother, Jared, (guest star Brendan Fehr) returns from his travels with some surprising news.
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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 (guest star Joshua Malina) at Havenhurst Sanitarium, they are confronted with suspects who are hard to characterize as either good or evil. Meanwhile, Jeffersonian intern Arastoo Vaziri (guest star Pej Vahdat) reveals a secret about his past.
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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 (guest star Carla Gallo) 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.
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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 Brennan's relationship, and will also give viewers the chance to see Zack Addy again, and Dr Saroyan as a New York Coroner.
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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 (guest star Robert Englund). Meanwhile, Hodgins spills a lab secret.
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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.
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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 woolly 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.
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A cabin burns down in the woods revealing the bodies of two witches, one modern-day and the other from the Salem Witch Trials. Meanwhile, when Hodgins and Angela get arrested and thrown in jail, Sweets and intern Clark Edison step into unfamiliar territory to help out the team.
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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.
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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.
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