Three months have passed since Brennan went into hiding after being framed for murder by Christopher Pelant (Andrew Leeds). Booth has been demoted to desk duty while Cam and her team are still reeling from Brennan's absence. The Jeffersonian team, with Angela's help, catches a break with the discovery of the body of Pelant's old guidance counselor and, with Brennan's help, they learn Pelant killed her and Brennan is cleared of the murder charge. Pelant is arrested but manages to escape from the
The Jeffersonian team investigates the murder of a high-powered divorce lawyer with a lot of enemies. The plot thickens when the team discovers that the attorney's wife and assistant have been hiding crucial evidence which could help solve the case. Meanwhile, Brennan tries to adjust to life after being on the run, and tensions start to rise between her and Booth as the impact of their three-month separation begins to take its toll.
When the Jeffersonian team investigates the murder of a man in an explosion, they find that the victim has a twin, complicating the investigation. Meanwhile, Booth is taken off field duty to work on getting the department's budget approved, possibly leading to a promotion. Sweets and a rookie FBI agent (Danielle Panabaker) instead lead the investigation.
The Jeffersonian team investigates the death of Jared Drew, an animal expo employee, and in the course of their investigation into his death, they enter the world of illegal animal trafficking. Meanwhile, Brennan thinks she would make an excellent presidential candidate, and Sweets and Daisy take on a big change in their relationship.
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 Brennan and him while Sweets searches for a new apartment, and Angela questions why she is using her artistic talent reconstructing the faces of dead people instead of following her passion.
After being inspired by basketball coach Phil Jackson, Brennan calls together the interns for a team building exercise to identify bones at the Jeffersonian that have remained unidentified for years. They soon discover the remains of one unidentified man who was found near the Pentagon days after the September 11 attacks. All of the Jeffersonian forensic team come together to help solve the case. When Booth realizes that the victim was a fellow Gulf War veteran who had become homeless and was th
Booth and Brennan investigate how a crime-scene cleaner’s body washed to shore inside a sealed pod. The Jeffersonian team pit their wits against their prime suspect, who also happens to be an experienced crime scene cleaner. Back at the lab, Angela and Hodgins discover Cam has been keeping a secret, a romance with a special someone.
A street artist, who is covertly plastering his art on a billboard, falls and lands directly into his own glue – and into human remains. So the team must not only figure out the identity of the remains, but must also find a strategic way to remove the part of the corpse that is still glued to the street artist. Meanwhile, Booth tries his hand at a comedy club’s "open mic" night in order to seek out potential suspects and Angela’s love of art leads her to become attracted to the street artist.
This episode is told and filmed from the point of view of the deceased victim. Everyone at the Jeffersonian begins wondering about life and death when the remains of a 14-year-old boy are found in a greenhouse. Angela calls upon Avalon Harmonia (Cyndi Lauper) when she believes that Avalon could help find out who murdered the young boy but, when Avalon arrives, everyone believes that she shouldn't be there; she later returns saying that she believes he's sad. Avalon finds that the young boy was s
Booth and Brennan go undercover in their previously used identities as "Buck and Wanda Moosejaw" (which they first used in the season 4 episode "Double Trouble in the Panhandle") at a ballroom dancing competition TV show when a contestant is found murdered, with jewels stuck to the body's bones. At the Jeffersonian, Hodgins and Wendell have difficulty removing the crystals from the bones, while Angela questions her career, hoping to revive her past as an artist.
Brennan and the team work on unraveling an archaeologist who seems to have been spun into a cocoon around a tree branch. He wrote novels on sensational topics and sold the items pertaining to the topic of his books for a price. Brennan and Edison compete on who will get to analyze bones that seem to indicate that they could be the victims of the world's first hate crime. Meanwhile, Brennan decides to curb her bad habits for the fear that her daughter Christine will inherit them.
Hodgins and Angela wake up to find a corpse in their bedroom, after being drugged. The personal attack on the team and Egyptian flower petals near their son makes them believe that Pelant is back. Despite Hodgins' desire to hunt Pelant down immediately and directly, Booth calls a closed-doors investigation and places the Jeffersonian on lock-down while the team is forced to use analog technology and not computers, to avoid being hacked by Pelant, as they try to figure out Pelant's next move. Boo
Booth and Brennan investigate two corpses found at the same burial site. The identifications reveal one was a terminal cancer patient and the other her doula, hired to help her process her diagnosis and the end of her life. The case causes Booth and Brennan to confront their individual and very different after-death arrangements. Back at the lab, Daisy returns to work her first case since her break-up with Sweets.
Angela goes undercover as a roller derby skater after one of the skaters is found dismembered. Meanwhile, Booth secretly does charity work for children with Neurofibromatosis (NF), and Wendell celebrates his 29th birthday.
Brennan is shot while working on a case late at night at the Jeffersonian, after having an argument with Booth at home. She is rushed to the hospital after Booth returns to the Jeffersonian and discovers her unconscious and gravely wounded. FBI Agent Olivia Sparling is brought in to assist the investigation. The Jeffersonian team is left dumbfounded by the lack of any bullets or an exit wound in Brennan. Meanwhile, while in surgery, Brennan hallucinates that she converses with her deceased mothe
The Jeffersonian team investigates the remains of a 15-year-old boy. Although his mother and 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. The investigation takes an ugly turn when an underage girl confesses to being raped and the deceased boy’s reputation is compromised. Meanwhile, with the case’s spotlig
When extremely educated new intern Dr. Oliver Wells (Brian Klugman) starts working at the Jeffersonian, his quick-learning, enthusiastic personality challenges Brennan as he gets under her skin with his eccentric but undeniable observations, causing her to try to be more open-minded about many scientific questions. Meanwhile, Booth worries she may have gone too far when she accepts the possibility of time travel as a factor in a murder investigation.
The Jeffersonian team investigates the death of Symchay Conteh, a young man whose remains were found in a barrel at a hazardous waste disposal facility. They discover that the victim was an immigrant and child soldier from war-torn Sierra Leone who was granted asylum in the United States as a young teenager in order to start a new life. The case gets personal for intern Arastoo, who sympathizes with the victim as he and his family had fled Iran during the chaos of the Revolution and the Iran–Ira
When the Jeffersonian team investigates the death of a former Marine sergeant whose remains were found burned to a crisp, they discover that she was discharged after a fist fight with another Marine. When Booth and Sweets go to question the other Marine involved in the altercation, they learn that Deanna was obsessed with the idea of the apocalypse, which leads the team to a following of doomsday preppers who become key suspects in her death. Meanwhile, Sweets thinks he has landed his dream apar
An undercover cop is found murdered with a bag of diamonds hidden inside his body. The cop had been investigating ATM robberies, and the Jeffersonian team investigates to determine whether the ATM robbers also murdered the undercover officer. Meanwhile, the Jeffersonian is the subject of a documentary by Andrew Jursic (Dave Thomas), to help raise money. While filming, Brennan worries she does not have a likable personality and Jursic shows an interest in Caroline Julian.
A body is found by treasure hunters under a patch of soil coated with mushrooms, the body is later discovered to be a woman who was a TV producer for a reality court show called Judge Trudy. Meanwhile, Brennan is concerned when she finds out her daughter Christine has bitten another child at daycare and Brennan is determined to find proof that a false assumption was made. Also, when Hodgins eats the last remnants of Finn's late grandmother's special hot sauce, he tries to chemically recreate the
The Jeffersonian team investigates the murder of Jack Spindler, a successful employee at a brokerage firm by day, but a stripper by night. When the team learns how Spindler's moonlighting affected his personal life, they start to question the people closest to him, including his stripper friend, Storm. Meanwhile, Booth's mother shows up after a 24-year absence in his life and makes a special request of him.
An ordinary murder case escalates into possible bioterrorism when the CDC brings in a body discovered at a biohazard disposal facility is found to have been infected with an unknown and potentially lethal virus. When Arastoo accidentally comes into contact with the remains, the team find themselves in unfamiliar territory as they work around the clock to identify the virus and solve the murder to prevent an outbreak.
Pelant returns, and Brennan begins to re-evaluate her relationship with Booth when evidence emerges that he could be Pelant's latest target after a series of murders are revealed to be connected to FBI agents with ties to Booth. Brennan surprises Booth under a gazebo and proposes. Sweets warns Booth that he and Brennan getting engaged with Pelant active could cause him to escalate. Angela determines that Pelant has access to every security camera with an internet connection. Later, Booth and Bre
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