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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 Angie 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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