Six months after starting a new life with her family, Brennan becomes interested in a case to which she has personal ties; an FBI investigation begins when Booth goes missing.
Booth's location and condition becomes more mysterious when it's discovered that FBI Agent Miller (Kim Raver) has been hiding vital information; Arastoo makes a significant decision.
When Brennan officially returns to work at the Jeffersonian and Booth resumes his position at the FBI, remains are found at a fish farm; Hodgins encourages Angela to exhibit her photography work; Cam faces a difficult decision.
Brennan enlists the help of a fellow forensic anthropologist in the investigation into the death of a real estate agent whose remains appear to have been destroyed by coyote-wolf hybrids.
While investigating a case involving a headless corpse, Brennan and Booth encounter Ichabod Crane and Abbie Mills searching for answers of their own; Brennan and Booth come up with Halloween pranks.
Two sanitation workers (Sal Vulcano and James Murray) find a U.S. senator's corpse in a street sweeper; Aubrey looks into Jessica's past.
An escape artist's corpse is found in the woods; Booth and Brennan try to decide if the tooth fairy should visit Christine; Angela works on her photography with Sebastian Kohl (Gil Darnell).
A political journalist is murdered after publishing an article regarding corruption in the NSA; Hodgins' paranoia increases as members of the team realize they are being monitored; Brennan plans a surprise for Booth; a Thanksgiving celebration.
Booth and Brennan go under cover at an Old West-style shooting competition; Angela and Hodgins talk about the future; Cam and Sebastian grow closer.
The team investigates a police officer's murder; the team decides what is important to their futures.
Hodgins navigates life in a wheelchair; when a public defender is murdered, several of her previous clients had motives to kill her.
The team investigates the death of a men's rights organization founder who may have been the victim of domestic abuse; Brennan loses her temper during an interrogation; Angela and the team struggle with Hodgins' bitterness.
The remains of an accountant for the state department are found in a hotel air conditioning unit; Booth finds an Army buddy and CIA agent, Danny Beck, removing evidence from the victim's condo; Brennan contemplates her future with Booth.
The investigation into the murder of a management consultant whose remains were partially eaten by bobcats leads to a marriage retreat site; Cam's identity is stolen; Sweets decides to take a leave of absence.
When the remains of a woman from a wealthy family are found in a national park, the team thinks she may be a victim of the Ghost Killer; Booth's career might be in for some changes.
The team investigates the death of an archaeologist who had just made an important discovery.
When Angela and Hodgins wake to find a corpse in their bedroom, they believe Pelant is behind it; against Booth's wishes, Angela and Hodgins start their own investigation.
The team investigates when two bodies are found at the same burial plot; Brennan and Booth discuss after-death arrangements; Daisy returns for the first time since the breakup.
When a female roller derby skater is killed and dismembered, Angie goes under cover to help solve the case; Cam tries to learn more about Booth's secretive hospital appointments.
While in the hospital after being shot at the lab, Brennan struggles with visions of her mother that defy her usual logic; evidence may link Brennan's attacker to the Jeffersonian.
As the team investigates the death of a seemingly innocent 15-year-old boy, they learn that he was involved in illegal activity.
When a well-educated but eccentric intern starts working at the Jeffersonian, Brennan tries to be more open-minded about scientific questions.
The team investigates the death of a young man whose remains were found at a hazardous waste disposal facility; Cam and Arastoo struggle to keep their relationship secret; Brennan and Booth try to decide where to take their vacation.
The investigation into the death of a former Marine leads the team to a group obsessed with preparing for the apocalypse; Sweets finds an apartment.
The team investigates when an undercover cop turns up dead with a bag of diamonds inside his body; Brennan struggles to be likable as the subject of a documentary film.
The team investigates when a TV producer is murdered; Christine is accused of biting a classmate; Hodgins uses his tools at the Jeffersonian to chemically re-create Finn's hot sauce.
The team investigates when a stock broker -- who moonlights as a stripper -- is murdered; after a 24-year absence, Booth's mother (Joanna Cassidy) shows up with a request.
The team tries to prevent a viral outbreak during an investigation into a journalist's murder, whose infected body is found at a biohazard facility; when Arastoo Vaziri is affected by the mutated virus, the only way to save him is to solve the case.