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The remains of a State Department accountant are found in a hotel's air-conditioning unit, but the investigation takes an unusual turn when Booth discovers that an old Army pal, CIA Special Agent Danny Beck, is also looking for clues. Meanwhile, Booth seeks advice from a friend, a former priest who runs a bar, about his relationship with Brennan, who is uncertain about their future together.
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Booth and Brennan go undercover as "Tony" and "Roxie" (their undercover personas from season 2's "The Woman in the Sand") at a marriage retreat site when evidence from the murder of a management consultant leads there. Meanwhile, Cam is the victim of identity theft and Sweets decides to take a leave of absence after feeling disconnected from his work.
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Sweets temporarily returns from his sabbatical to assist the Jeffersonian team investigate the murder of a Mexican gang member, after he discovers that one of the young kids he has been volunteering with is a son of a gang member.
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The Jeffersonian team use a cadaver to stage a murder in a way that mimics how Christopher Pelant would, hoping to draw him out. Pelant figures this out and in turn murders FBI agent Hayes Flynn, who helped the Jeffersonian team set up the staged murder scene. Pelant is able to sneak into the Jeffersonian and tells Brennan that several unsolved murders were done by a female serial killer, and only he can help her solve them. Using evidence from Flynn's murder, Brennan tracks Pelant to an abandoned power plant. When Booth arrives, Pelant has Brennan and is threatening to blow up the plant, but Booth is able to shoot and kill Pelant. With Pelant now dead, Booth proposes to Brennan, who accepts.
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A man is found on a cliff side, hanging from climbing gear and has been partly eaten by a nearby hawk. After being diagnosed with cancer he began a very profitable business selling self-help videos online. The case takes a different turn when Angela discovers a video of him punching martial artist Chuck Liddell. Sweets is back permanently but is less than pleased when Booth shows him VAL, a new computerized profiling system his department recently acquired for him. Back at the lab, Dr. Wells continues to irritate and impress Cam with both his tactlessness and brilliance. Meanwhile, Brennan and Booth plan their wedding.
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During Booth and Brennan's wedding rehearsal, they receive a call that a body has been discovered. The rest of the Jeffersonian team try to keep the details of the investigation from Brennan so she can focus on her wedding. Cam enlists the interns to solve the case. After the church they were going to get married in was burned down, Angela plans a new wedding. Booth and Brennan are married in the rose gardens of the Jeffersonian, with several family and friends in attendance, including Brennan's father, Booth's mother, grandfather, and son.
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Brennan and Booth spend their honeymoon in Buenos Aires, but end up helping with a local murder investigation. They assist Raphael Valenza, a local detective and fan of Brennan's novels (which are very popular in Argentina), in solving the murder of a Nazi war criminal whose remains were found in an historic mass grave. Meanwhile, Angela and Hodgins take care of Christine while Brennan and Booth are away and discuss having a second child.
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The Jeffersonian team investigates the murder of Sean Nolan, a failed model whose body is found intertwined in a beaver dam. The team soon discovers that Nolan's fruitless modeling career left his sperm donations as his only source of income. However, when the team learns that he falsified records, they start to suspect anyone who was jilted by his donations. Meanwhile, Brennan struggles with social niceties and tact when she is drawn into a feud with author Tess Brown and Hodgins gets in touch with his motherly instincts when he plays host to a fly larva.
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Brennan serves as a juror on a case in which a professional soccer player, Peter Kidman, is accused of murdering his wife. The jury renders a not guilty verdict due to no evidence tying him to the murder. However, when the Jeffersonian team receive a body that turns out to be Kidman's best friend, who was planning on changing his testimony in the trial that would have helped convict Kidman, Brennan rejoins the team and they try and prove that Kidman killed his wife and best friend. Meanwhile, Angela discovers who is behind Cam's identity theft, and Cam identifies her as her old college roommate.
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The Jeffersonian team investigate the murder of a food scientist whose remains were discovered throughout several cans of stew that were served at a school cafeteria. Meanwhile, Angela, Brennan, Cam, Caroline, and Daisy go out for Brennan's post-wedding bachelorette party, leaving Hodgins and intern Oliver to continue to solve the case.
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The Jeffersonian team investigate the murder of a young woman who was a highly skilled gymnast. Her remains were hit by lightning and scattered throughout a park. Several fellow gymnasts are suspects as the victim was nationally ranked No. 1. Meanwhile, Cam comes face-to-face with her former college roommate, who stole her identity and who has been brought in by the FBI. Olympic gymnast McKayla Maroney guest stars.
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Bones has nightmares about what Pelant told her about the female serial killer, "The Ghost Killer". Remains of a girl named Lana Brewster are left at Booth and Brennan's doorstep with a note saying to solve her murder. The dreams start to interfere with her job and Cam gives the remains to Clark. Brennan becomes obsessed with the Ghost Killer and believes the murder of Lana is connected to the Ghost Killer. One of the suspects, Trent McNamara, an old childhood friend of Hodgins, is found in his home having supposedly committed suicide.
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The remains of country singer-songwriter Colin Haynes are found in a garden. After Wendell breaks his arm in a hockey game, Brennan and Cam examine his X-rays and discover that he has a rare form of bone cancer, known as Ewing's sarcoma.
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When a famous chess master is found in pig slop, Sweets goes undercover at a chess club to investigate. The prime suspect proves to be challenging and Sweets and Booth each lend their unique perspectives in order to extract a confession. Meanwhile, Cam receives an award but is hesitant to take it unless both Brennan and Angela are honored as well. Dr. Douglas Filmore, a Canadian forensic podiatrist, returns to serve as the case's intern.
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The remains of a kidnap victim are found buried at a park. Hodgins learns a secret about his family which both excites and distresses him. Booth and Brennan discuss how to handle their finances after Brennan receives a $75,000 advancement from her book sales and asks a reluctant Booth to cash the check and decide what to do with it.
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A victim is found stuffed in a duffel bag floating in a lake. Booth reunites with his old friend CIA Agent Danny Beck after discovering that the victim is a female Afghani refugee and informant whom Beck had helped gain political asylum in the United States. Brennan and Booth have a disagreement when she learns that her insurance company is charging her a higher premium as they deemed her more "at risk" when out in the field compared to Booth and she plans to challenge it. Back at the lab, Daisy seems to be under the weather and is unable to concentrate.
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The corpse of a missing repo man with a troubled past is found in a septic tank. The Jeffersonian gets a new Cuban intern Rodolfo Fuentes, who attempts to charm the ladies, much to Booth's ire. Booth and Brennan discuss whether or not Christine should be given a religious upbringing.
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An actor from a popular children's television show is found murdered and his corpse covered in kudzu. Clark has written a new fiction novel and asks his colleagues for their opinions. Booth and Brennan discuss party plans for Christine's first birthday.
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When a man who collects artifacts attends his own funeral, the team must determine who was cremated in his place, leading to the discovery of a possible multiple murderer. Meanwhile, Finn and Hodgins' hot sauce business takes off but Michelle returns to Washington D.C. with distressing news for him.
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Remains found in a log in Great Falls Park belong to an art school dropout suffering from lupus who was using marijuana to ease her pain, but evidence suggests that her death is linked to her work at a dispensary. Meanwhile, Wendell reveals information about his illness which may cost him his job and Booth gets ready for his yearly FBI competency test.
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A woman's remains are found in a swamp. The case takes a bizarre twist when the team discovers that the victim was cryogenically frozen before her death. Meanwhile, Cam is nervous about meeting Arastoo's parents and Booth may be up for a promotion.
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The body of Stephanie McNamara, sister of Trent McNamara (from the episode "The Ghost in the Killer"), is found in a swamp. Given the high profile and financial wealth of the McNamara family, the Deputy Director of the FBI takes an interest in the case. The circumstances surrounding Stephanie's death lead the team to believe that the "Ghost Killer" is back. The identity of the murderer is revealed as the McNamara family's decades-long secrets come to light.
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The body of a college swim coach is uncovered at the bottom of a well. Sweets fills in for Booth, who has to testify at a congressional subcommittee. As he and Brennan sift through the suspects and evidence, they realize that the swim coach has been living a secret life off campus. The Jeffersonian gets a new intern Jessica Warren.
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The charred corpse of a conspiracy blogger is found in his trailer. The case turns out to be much bigger when Booth and the Jeffersonian team uncover a complex web of conspiracies and blackmail involving that some of the country's top government and business leaders, including the McNamara family. Classified information from his military service is exposed during Booth's congressional hearing, setting off a series of events which put his career into question. Meanwhile, the "squint squad" race against the clock to find out who is behind the blackmail and targeting Booth.
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