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There is no Next Episode of Bones planned.
Group of teenagers are driving on the freeway when a skull smashes through their windshield. At the Jeffersonian lab, Brennan tests out a young forensic anthropologist to replace Zack, who has left for Iraq, and she and Cam examine the skull in question. They find it has marks made by human teeth, suggesting cannibalism. The team identifies the victim, a known violin protégé who disappeared after a concert. On a quest to find out what happened to him, Brennan and Booth go into the field. A trail of suspects leads them to a strange cannibalistic society, and the team must string together a gruesome and cryptic series of crimes - provided that Brennan and Booth can survive the newfound tension between them. Meanwhile, Cam suggests that Angela hire a private investigator to track down her ex-husband so she can annul her previous marriage and marry Hodgins, a task easier said than done.
When a soccer mom gets blown up in her minivan, Brennan and Booth are on the case to figure out who would want to murder a seemingly innocent and inconspicuous suburbanite. Upon investigation, the team discovers that the mother, June, had been a member of the National Liberation Army, a group of young radicals from the 1970s, and that the FBI had been looking for her for nearly thirty years. When the team learns that June may have been on the verge of turning herself in for a violent crime she was involved in while part of the NLA, the motives for her murder become even more complicated. Meanwhile, Brennan visits her father in prison and questions his reasons for wanting to see her, and Booth lends his advice on the situation. Back at the lab, Hodgins is rendered speechless by a particularly beautiful FBI bomb expert working on the case.
When an 11-year-old camper finds the decomposed body of a man in the woods, feet removed and arms bound, the team goes in to investigate. The autopsy leads Brennan and Booth to a lodge in Virginia not far from where the victim died. It turns out the lodge is used as a "Pony Play" S&M retreat where women act as jockeys and men act as their horses. Brennan and Booth's questioning leads them to suspect a number of people, including the victim's wife and his female "jockey" lover. However, Zack and Hodgins uncover evidence that makes deciphering the killer more difficult than initially expected. Meanwhile, Angela agrees to go under hypnosis in an effort to discover the name of her previous husband so that she can divorce the mystery man from her past and marry Hodgins, but she finds it difficult to fall under the hypnotist's trance.
Booth and Brennan go in to investigate when teenagers find a severely decomposed body on the grounds of the V.A. hospital. The man is identified as Franklin Curtis, founder of an organic supermarket chain. The team is puzzled when the body's high temperature reveals that it had been cooked or incinerated. As they attempt to pin down an initial cause of death at the lab, Brennan and Booth question potential suspects around Curtis' farm. They suspect foul play by a rival farmer from whom Curtis was trying to buy land to turn it organic. In their investigation, Booth and Brennan also discover that Curtis was a well known philanderer. When the flesh of another body is identified with Curtis', the team must investigate a possible double homicide. Meanwhile, Booth and Brennan are assigned to a new - and very young -psychiatrist, Dr. Lance Sweets. He warns them that the FBI may separate the two unless they undergo further psychiatric counseling, and they reluctantly cooperate.
When a terrified young Halloween reveler finds the mummified remains of a teenage girl in a Halloween pumpkin patch maze, Brennan and Booth are called to the scene to investigate. They are perplexed by the fact that the girl appears to have been deceased for at least a year, while Hodgins discovers her body is covered with spider bites. Booth and Brennan later receive word of a second mummy found at Halloween amusement park funhouse, and it appears the victim, another teenage girl, was killed on Halloween approximately two years prior. As the team questions a variety of ghoulish amusement park employees, from the grim reaper to a zombie, they get word of a third teenage girl who has gone missing. Booth and Brennan realize that they have until Halloween to find her before the killer strikes again. Meanwhile, the team gets decked out in costume for the annual Jeffersonian Halloween Ball, and they encounter a few scares of their own.
The charred remains of a young Jeffersonian intern, the daughter of a highly respected former Jeffersonian scientist, are found in the building's incinerator. With the case hitting so close to home, the team has no choice but to suspect their own colleagues and question everyone from the upper echelons of the Jeffersonian scientists to the victim's fellow interns. When they learn that the intern had been working on artifact authentication for the Widow's Son serial killer case, they begin to wonder if her involvement could have put her life in danger. But when they discover a romantic link between the intern and a Jeffersonian employee, the motives behind her murder become even more complicated. Meanwhile, Booth agrees to pose as Cam's boyfriend and accompanies her on a family get-together, eliciting more attention than he bargained for from Cam's sister.
Group of high school alumni gather to unearth a time capsule buried 20 years prior, only to find the body of one of their former teenage classmates inside. The victim, identified as a shy, ostracized classmate, leads Booth and Brennan searching through the class of 1987's high school secrets as they rehash some high school memories of their own. With psychological profiling advice from their young therapist, Dr. Sweets, the team's investigation has them exploring timelessly familiar high school stereotypes - the geeks, the outcasts, the jocks and the cheerleaders - in an effort to discover the murderer.
After construction workers find the body of an archbishop whose kneecaps were surgically removed, the team is back on the case of the Widow's Son serial killer. When Angela discovers what appears to be a victim tree in the evidence vault, the team realizes the killer employs a systematic pattern in selecting victims. With a musician and an archbishop the first to go, the team tries to predict who might be next and how they can stop the killer before he strikes again. Brennan and Booth continue to see Dr. Lance Sweets, who has some helpful psychological insights into the Widow's Son's motives. Meanwhile, Brennan's brother, Russ, comes out of hiding when he finds out that his girlfriend's daughter is extremely sick, but his appearance causes Booth to intervene with Brennan's family once again.
The body of a man with a white beard and a tailor-made Santa costume is discovered in the sewer near a D.C. mall just three days before Christmas. As the team gathers forensic evidence, the victim seems to match the legend more closely each step of the way. Booth and Brennan discover the man, whose legal name was Kristopher Kringle, was a well respected Santa Claus impersonator, employed by a local "Rent-A-Santa" business. When Booth and Brennan inspect Kris' apartment, not only do they find his place decked out with holiday cheer, but they also find thousands of dollars stashed in a dresser drawer. As Christmas Day approaches, the Jeffersonian team works to find out who would have wanted this true-to-myth Santa dead. Meanwhile, Brennan visits her father in jail and plots a not-so-traditional Christmas reunion, and Booth and Brennan find themselves in close quarters with the mistletoe just overhead.
When a young couple decides to go skinny-dipping in a hot spring, their spontaneity is ruined when they find the remains of a skeleton in the mud. Brennan and Booth soon discover the skeleton is that of Tripp Goddard, a professional motorcycle racer who just won the Super Grand Prix. The team immediately suspects Danny Fitz, the runner-up in the race and Tripp's main rival, to be the murderer. But just when Brennan and Booth think they have it solved, a fiery motorcycle crash claims another victim, and the circumstances seem far from accidental. Meanwhile, Dr. Lance Sweets forces Brennan and Booth to join him on a double-date in an effort to encourage them to interact in a social setting, away from any of their cases.
Brennan and Booth visit a college campus where human remains are found under the bleachers of a basketball court. Although the body had been crushed beyond recognition underneath the bleachers, a gold "#11" necklace identifies the victim as RJ Manning, the star point guard of the school's nationally ranked basketball team. After reconstructing RJ's skull, the team determines that he was dead before the bleachers crushed him. Brennan and Booth navigate the world of big-time collegiate basketball and interview multiple leads to find out who could possibly have benefited from RJ's demise. After investigating those with the closest ties to RJ, including his faithful girlfriend, his future basketball agent and his replacement on the school's team, Brennan and Booth uncover several different plausible motives for RJ's murder. Later the team discovers that RJ may have been caught up in a rather risqué situation at the time of his death, and they wonder if more than one person could have been involved in his murder. Meanwhile, Hodgins attempts to take his relationship with Angela to the next level, but his courting methods prove to be far less tactful than his scientific ones.
Booth and Brennan investigate the scene where a car was run off the road and the victim's body deliberately burned beyond recognition. When the team hears muffled whimpering during the site investigation, they find the victim's baby miraculously perched in a tree above the scene of the crash. The team designates Brennan as the infant's caretaker, but when the baby swallows a key piece of evidence, they question her nurturing skills. The team soon identifies the victim as a laborer who worked in a tire-recycling factory in a small, impoverished town in Virginia, and Brennan and Booth venture out to investigate who might have wanted her dead. Their suspicions range from her deadbeat husband to the impecunious habitants of her town. Meanwhile, the team is fascinated by the presence of a baby in the lab and its affinity for Brennan.
Brennan's father, Max, is put on trial for the alleged murder of FBI Deputy Director Robert Kirby, and the entire Jeffersonian team, excluding Brennan, are called to be expert witnesses for the prosecution. As Booth and the rest of the team grapple with trying to be impartial knowing that their testimony could send Brennan's father to Death Row, Brennan insists that everyone participate objectively in the trial. With Brennan serving as a forensics advisor for the defense, she must rely not only on her expertise as an anthropologist but on her dedication to her family to find a way to exonerate her father.
Brennan and Booth probe the murder of an aspiring young singer, Tommy Sour, whose body was discovered on a rural roadside. They investigate the singer's many fans and foes in the music circuit, and, in particular, one obsessed woman who redirects her affections toward Booth after Tommy's death. As the team searches to find out who silenced Tommy once and for all, a shocking occurrence may change the Jeffersonian team forever as one member is caught in the line of fire.
When a human jawbone shows up at the Jeffersonian, Brennan and the team quickly realize that the Gormogon serial killer has struck again. In a shocking turn of events, an explosion in the lab sends Zack to the hospital, and it is discovered that Gormogon's silver skeleton goes missing from the basement vault. Every Jeffersonian employee soon becomes a suspect, with the very real possibility that one of their very own may be working as an apprentice to the twisted and elusive serial killer.