Bones returns from Guatemala as Booth is finally cleared for duty; Booth is anxious to prove he's fully recovered, even accepting help from Angela's psychic. Things take an interesting turn when the psychic informs them that there is a mass grave underneath a fountain.

A diamond courier carrying a briefcase is killed. State Department requests discretion while investigating due to National Security concerns. Meanwhile, Wendell loses his scholarship, and Booth tries to relearn plumbing techniques.

Bones and Booth investigate the murder of an Amish piano prodigy.

A corpse found roasted in a neighborhood party barbecue pit is identified as missing dentist Kurt Bissette. He had not only upset neighbors with his windmill and by nearly poisoning the gay couple's dog but probably was a blackmailer. Trey Johnson, the owners society's handsome young gardener, isn't the only one enjoying residents' infidelity, which isn't the only possible secret or motive either. Meanwhile young Parker seems worried about Booth's lack of female company. Sweets figures out why Arastoo faked his accent.

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.

When the remains of a local chicken farmer is found, the Jeffersonian team is brought in on the case. The team must question the farmer's many enemies in order to solve the case. Meanwhile, Angela launches her own animal-rights campaign.

Booth, still suffering from his brain surgery, has to get re-certified for FBI marksmanship. Meanwhile, the team investigates the remains of a little person discovered in a sinkhole. The victim, Bryce DaFonte, also known as "The Iron Leprechaun," competed in a popular wrestling league, the popularity left him with many enemies.

In Howard Fileman's house, which is for sale, estate agent Katie Selnick and two prospective buyers discover a corpse, charred except for a fat foot. Clever forensics gradually show it was actually two people, a fat man and PriceCo saleswoman Meg Tracy, who recently lost half her excessive weight and met her lover in a fetishist club. Seeley however is greatly distracted by a surprise visits from Hank 'Pops' Booth, who left his retirement home after hitting a male nurse and now tries to "correct" Booth's life, but rather lost control of his own.

Mailman Steve Rifton's corpse is found in frying fat, hence extremely decayed over two weeks. He was reported missing for three months. The highly intelligent man's passion was the computer game Punky Pong. He recently lost the world record, which was bitterly contested. Both motive and means require several theories based on forensic findings until things start fitting. Meanwhile Jeffersonian intern Colin Fischer gets three Avatar tickets, which also excites Hodgins and Sweets, so they cover for each-other to take turns standing in line for the best seats. Colin's tent however offers an unexpected alternative 'entertainment' for two.

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.

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 come clean about their relationship.

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, Booth's 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.

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 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, returns from his travels with some surprising news.

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.

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.

The milestone 100th episode takes viewers back in time six years as Brennan and Booth recount the first case they worked on together. With Sweets finishing his book on their partnership, Brennan and Booth take this opportunity to set the record straight. A young and rebellious FBI Agent Booth seeks the help of an team of anthropological scientists and a street artist to find the evidence that will prove his high-profile suspect guilty. Although in unfamiliar territory, Dr. Brennan, her grad student Zack and Hodgins get right to work, impressing Booth with their knack for uncovering new leads and substantiating his theory about a well-connected district judge. While the case cements a foundation for a successful future partnership, it also reveals the convoluted romantic beginnings of the formidable duo - whose feelings for each other almost destroyed the team but still linger years later.

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 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.

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.