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The body of a high school guidance counselor may be Brennan's ticket home, but first the team must determine if Christopher Pelant is still controlling events behind-the-scenes. Meanwhile, Brennan and her father manage to elude the feds, and the FBI puts the Jeffersonian under the microscope.
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Booth and Brennan investigate the murder of a famous divorce attorney who was in the midst of his own divorce. Unfortunately, the interviews highlight their own relationship struggles after three months apart.
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The team investigates a man who should be dead from a bomb explosion, but whom they find living with his wife when they come to notify her of her loss. Meanwhile, Sweets breaks in a new partner from the FBI.
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The investigation into the mauled body of a day laborer at an animal expo leads the team to an animal trafficking operation, the operator of which is also the owner of the expo. Elsewhere, Brennan looks at a political career, while Sweets and Daisy face a major change in their relationship.
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The Jeffersonian team investigates the death of a woman whose body was found mutilated and discarded in a city garbage can. Meanwhile, Booth invites Sweets to stay with him and Brennan while he searches for a new apartment.
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While investigating the remains of bodies that have been deemed unidentifiable, five “squinterns” uncover the identity of a man who died as a result of the 9/11 terrorist attacks, propelling the Jeffersonian team to determine if he was a perpetrator or a victim.
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When a crime scene cleanup expert’s remains are found mysteriously sealed in an impenetrable pod that washed up on the beach, the team tackles one of their most challenging investigations. Meanwhile, Angela and Hodgins learn of a secret romance in which Cam is involved.
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A street artist who is plastering his work on a billboard falls into his glue—and onto a corpse—so the team try to get him unstuck from the remains as they also work to identify the body. Meanwhile, Booth takes a stab at stand-up comedy at a club's open-mike night to look for suspects; and Angela finds herself attracted to the street artist.
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Brennan and Booth investigate the remains of a young boy found in an abandoned greenhouse. But when it seems the boy's soul remains alive, Avalon Harmonia returns and attempts to help the deceased boy cross over. Meanwhile, the team start to question his/her beliefs about life after death.
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An apparently diamond-encrusted corpse is found, a ballroom dancer, and she died just before a major competition on the TV show “Dance to the Top”. Booth and Brennan go undercover as a dance team and audition for the show. Meanwhile, Hodgins and Wendell desperately try to find a way to clean up the victim’s crystal-encrusted bones. Angela realizes that she’s let her dream of being an artist slip away while working at the Jeffersonian, and starts to re-evaluate her life.
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A cocooned skeleton is found in a tree. The victim is identified as James Sutton, famed adventurer and archaeologist, who made a genuinely significant discovery – human bones, thousands of years old. Brennan and Dr. Edison fight over custody of the ancient bones… which are not only a scientific curiosity, but also pose a millennia-old murder mystery.
Meanwhile, Brennan is frustrated that baby Christine isn’t interested in peek-a-boo, which leads Booth and Sweets to worry that Brennan is being overcompetitive and may place too much pressure on Christine as she grows up.
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After Hodgins and Angela were drugged and woke up to a bloody corpse hanging in the canopy of their bed and flower petals around their son Michael’s crib, they are forced to believe that Pelant is back for revenge against Hodgins. Although Hodgins wants to go after Pelant directly, Booth knows it’s best to work within the system and not go against protocol. As the Jeffersonian team investigates the corpse, they discover the victim was a Special Forces agent working for the world’s biggest supplier of mercenaries, and Angela and Hodgins decide to start an investigation without the rest of the Jeffersonian team for the sake of their family.
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The Jeffersonian team investigates the remains of two bodies that were found at the same burial plot: one of a female cancer patient; the other, the cancer patient’s “doula,” who was guiding her through her grieving process with the illness. Meanwhile, with a spotlight on the case, Brennan and Booth start discussing their individual choices for after-death arrangements. Also, Daisy Wick returns for her first case after her break-up with Sweets.
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Brennan and Booth investigate the death of a female roller derby skater whose body was dismembered. In order to get more answers, they enlist Angela to go undercover as a derby skater. Meanwhile, Cam tries to uncover the details behind Booth’s secretive hospital appointments.
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When Brennan is shot by an intruder at the Jeffersonian, the team rushes to solve the case... while a flatlining Brennan finds herself speaking with her late mother.
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The Jeffersonian team investigates the remains of a 15-year-old boy. Although his mother and a few close friends saw him as intelligent with poor social skills, the team discovers that this seemingly innocent boy was actually involved in illegal activity and had attended a high school party two weeks prior where drugs were present.
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When extremely educated new intern Dr. Oliver Wells starts working at the Jeffersonian, his enthusiastic personality and eccentric but undeniable observations get under Brennan’s skin and cause her to try to be more open-minded about scientific questions. But Booth worries she may have gone too far when she accepts the possibility of time travel as a factor in a murder investigation.
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The team investigates the death of Symchay Conteh, a young man whose remains were found in a barrel at a hazardous waste disposal facility. Meanwhile, as the team gets deeper into the investigation, Cam and Arastoo find it even more difficult to keep their relationship a secret and Brennan and Booth try to decide where to go on vacation.
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The death of a former female Marine sergeant whose remains are found charred due to an explosion leads Booth and Sweets to a group of doomsday preppers, of which the victim Deanna was a member. Meanwhile, Sweets finally finds an apartment and moves out of Booth and Brennan's home.
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An undercover cop is found murdered with a bag of diamonds hidden inside his body. The cop had been investigating ATM robberies, and the Jeffersonian team investigates to determine whether the ATM robbers also murdered the undercover officer. Meanwhile, the Jeffersonian is the subject of a documentary by Andrew Jursic, to help raise money. While filming, Brennan worries she does not have a likable personality and Jursic shows an interest in Caroline Julian.
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A body is found by treasure hunters under a patch of soil coated with mushrooms, the body is later discovered to be a woman who was a TV producer for a reality court show called Judge Trudy. Meanwhile, Brennan is concerned when she finds out her daughter Christine has bitten another child at daycare and Brennan is determined to find proof that a false assumption was made. Also, when Hodgins eats the last remnants of Finn's late grandmother's special hot sauce, he tries to chemically recreate the sauce.
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A stockbroker moonlighting as a stripper is found at a construction site. This leads to many awkward conversations around the lab and Bones' surprising (and blunt) opinions about "exotic dancers". Meanwhile, Booth's mom Marianne shows up after 24 years to invite him to her wedding.
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An ordinary murder case escalates into possible bioterrorism when the CDC brings in a body discovered at a biohazard disposal facility is found to have been infected with an unknown and potentially lethal virus. When Arastoo accidentally comes into contact with the remains, the team find themselves in unfamiliar territory as they work around the clock to identify the virus and solve the murder to prevent an outbreak. After Arastoo is saved and the killer identified, Brennan surprises Booth under a gazebo.
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Pelant returns, and Brennan begins to re-evaluate her relationship with Booth when evidence emerges that he could be Pelant's latest target after a series of murders are revealed to be connected to FBI agents with ties to Booth. A threatening phone call from Pelant causes Booth to withdraw accepting Brennan's marriage proposal, and he fears telling her the truth will endanger her and Christine.
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