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In the Season 11 finale, the search for the Puppeteer, a serial killer who turns his victims into marionettes, continues, but Brennan can't shake her guilt of failing to catch the perpetrator due to her brief period of retirement.
A body is discovered at a glass recycling plant with a diamond in its jaw, and a French inspector works with the team as they each pursue their suspects. Elsewhere, Hodgins has ghost issues, and Booth is diagnosed with an eye condition.
The team investigates the murder of a billionaire explorer who went missing 10 years earlier, and whose death may involve one of the team members. Meanwhile, Cam's sister arrives to help with the wedding, but brings with her some family history.
The death of a professional hockey player is investigated after his headless corpse is found in a river, and Booth's love of the sport proves to be an asset in the case, but it also reunites him with an old rival and puts him back on the ice. Meanwhile, Hodgins and Oliver compete to build a drone to retrieve the victim's head; and Brennan and Booth try to get their home organized and free of clutter.moreless
As part of a promotion for the Jeffersonian's Medico-Legal lab, a film crew follows the team as they investigate a murder case involving a corpse buried in a landfill more than 10 years ago, and each member provides commentary in their fields of expertise.
While Brennan is at home with a cold, the team looks over the body of a secret service agent which leads them to wonder if his death was personal or was part of an attempt to kill the president.
A body found in a rat lab at Lynwood University turns out to be the head of a male a cappella group who recently ejected one of their best singers. Meanwhile, Booth hopes to go on a summer vacation with Parker; a new intern joins the Jeffersonian; and Aubrey's college experience becomes a topic of interest.moreless
The team discovers that their latest victim was both a private investigator and a fixer, giving them a large list of suspects. Meanwhile, Hodgins tries his best to apologize to Angela for being a jerk to her, but she thinks that he might be trying too hard. Also, Brennan makes a bet with Wells when Christine is suspected of cheating on her report card.moreless
The remains of a female felon are found during a mudslide and Booth discovers that one of the suspects is someone he met during his time in prison. Meanwhile. Brennan must attend a hearing after punching a suspect.
A social worker's remains are found, but evidence suggests the victim had been dead for months before the body was dumped in a park, and the case gets even more twisted when it's linked to a serial killer known for desecrating corpses. Meanwhile, Booth and Aubrey hope a behavioral analyst can provide some clues about the murderer; and Cam tries to sort out her romantic life.moreless
The team tries to solve the murder of a man who was the head a men's rights organization. Meanwhile, Hodgins' bitter attitude about being in a wheelchair causes a strain on the working environment and his marriage.
Hodgins' rehab continues eight weeks after the explosion that left him paralyzed, but he's not quite ready to accept spending the rest of his life in a wheelchair. Meanwhile, Brennan and Booth investigate the death of a public defender whose long list of clients reveals plenty of murder suspects.
The investigation of a murdered police officer gets some help from a behavioral analyst. Meanwhile, Cam faces some difficult decisions in her personal life.
Brennan and Booth go undercover at an Old West-theme shooting competition. Meanwhile, Angela and Hodgins discuss their future and what it holds for their family; and Cam gets to know Sebastian better.
Booth and Brennan investigate the death of a journalist who had just published an exposé of the NSA – a case tailor-made for Hodgins' conspiracy theories. Elsewhere, everyone gathers for Thanksgiving dinner, and Brennan tries to surprise Booth.
An escape artist's body is found in the woods, and it's revealed that he may have had enemies in the magic community. Meanwhile, Brennan and Booth ask their friends to opine on their tooth-fairy debate; and Angela continues to work on her photography with Sebastian Kohl.
The body of a U.S. senator is found in a street sweeper by an unusual pair of sanitation workers. Meanwhile, Aubrey pursues a relationship with "squintern" Jessica, but he also secretly digs into her past to make sure there are no skeletons in her closet that could ruin his dreams of a political future.moreless
In part one of the two-part crossover event, Brennan and the team work to identify a 200-year-old headless body and its relation to a recent murder victim. New FBI Agent Abbie Mills appears at the Jeffersonian with Ichabod Crane in tow, and both teams must find a way to work together as Brennan's science and logic clashes with Mills and Crane's belief in the mystical. Elsewhere, Booth and Brennan compete for best Halloween prank against each other.moreless
A real-estate agent's remains are discovered in a forest and show signs of being partially devoured by coyote-wolf hybrids, so Brennan solicits help from an older, distinguished forensic anthropologist, who amazes the staff with her decades of experience and surprising knowledge of fantasy football, with which the victim was heavily involved and even linked him to a social-media feud with an NFL star.moreless
Booth and Brennan deal with changes when they return to their jobs, but a new case helps ease the transition. Remains at a fish farm raise suspicions when it turns out organs have been removed from the body, and Angela's tracking of illegal organ sales helps the team find the perpetrator. Meanwhile, Cam is conflicted by her decision, and Booth finds that Aubrey has made himself at home in Booth's office. Elsewhere, Hodgins encourages Angela to show her art professionally.moreless
Booth is still missing, but the team learns that Agent Miller has hidden information about his whereabouts and physical state. Meanwhile, a digital forensic scientist helps Angela try to decipher information pertaining to Booth's location and the circumstances of his disappearance; and Arastoo makes a decision that will change his and Cam's personal and professional relationships.moreless
In the eleventh season premiere, Booth, Brennan and family have gone in search of a crime-free life, but their ties to the Jeffersonian are only frayed. Brennan returns to the institute when a case involves her and Booth. Booth, however, has disappeared, prompting an FBI investigation and an agent who looks at the team as suspects. Meanwhile, Arastoo, who has taken over Brennan's duties in her absence, hopes that the lead position becomes permanent. Elsewhere, Brennan meets one of Booth's family members.moreless