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The Partners in the Divorce
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.
The Method in the Madness
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.
The Future in the Past
Having been accused of murder, Brennan is on the run from the FBI, with help from her father Max. Booth and the Jeffersonian team are convinced evil tech genius Christopher Pelant has manipulated key evidence in the case to pinpoint Brennan as the prime suspect. Then, an anonymous tip leads the team to the remains of a high school guidance counselor that may hold the key to proving Brennan's innocence.
The Gunk In The Garage
After an explosion occurs in a hotel garage, the Jeffersonian team must research the remains found at the crime scene in order to match them to the victim. The investigation only gets trickier when they discover that the man whom they thought was dead is actually alive. Meanwhile, Booth has to take on a desk assignment to get the department's budget approved in order to land a promotion, so Sweets is given a temporary partner, FBI Special Agent Olivia Sparling.
The Tiger in the Tale
the team believes some exotic animal played a crucial role in a victim's death.
The Patriot in Purgatory
Brennan becomes fascinated with basketball and the underlying concepts behind Phil Jackson's philosophy of "teamwork," she calls upon five of her best "squinterns" to complete the task of identifying remains that have been deemed unidentifiable. During their investigation, the squints uncover the identity of a man who died as a result of the 9/11 terrorist attacks, which propels the team to determine if he was a perpetrator or a victim.
The Bod in the Pod
The Jeffersonian team investigates the death of a crime scene cleanup expert whose remains are found mysteriously sealed in an impenetrable pod that washed up on the beach. Meanwhile, Angela and Hodgins learn that Cam is involved in a secret romance.
The But in the Joke
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.
The Ghost in the Machine
The team investigates the death of a boy that was not prepared to cross over.
The Diamond in the Rough
The team investigates the death of a professional ballroom dancer.
The Archaeologist in the Cocoon
The Jeffersonian team investigates the murder of a well-known archeologist with a very questionable reputation.
The Corpse on the Canopy
Angela and Hodgins wake up to find a corpse of a Special Forces agent dangling in the canopy of their bed. They soon discover it is the work of Pelant, who has come back for revenge. Booth tries to convince them to work within the team, but Angela and Hodgins decide to start an investigation of their own to protect their family.
The Survivor in the Soap
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 from Sierra Leone working numerous part-time jobs in order to make ends meet Meanwhile, as the team gets deeper into the investigation, Cam and Arastoo find it even more difficult to keep their relationship a secret and Brennan and Booth try to decide on a vacation destination.
The Twist in the Plot
The Jeffersonian team investigates the remains of two bodies that were found at the same burial plot: one of a female cancer patient; the other, the cancer patient's "doula," who was guiding her through her grieving process with the illness. Meanwhile, with a spotlight on the case, Brennan and Booth start discussing their individual choices for after-death arrangements. Also, Daisy Wick returns for her first case after her break-up with Sweets.
The Doll in the Derby
Brennan and Booth investigate the death of a female roller derby skater whose body was dismembered. In order to get more answers, they enlist Angie to go undercover as a derby skater. Meanwhile, Cam tries to uncover the details behind Booth's secretive hospital appointments.
The Shot in the Dark
Brennan has a near-death experience while at the hospital, having visions of her mother that defy her usual logic.
The Friend in Need
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 spotlight on deception, intern Finn Abernathy contemplates telling Cam that her daughter Michelle is in town visiting for the weekend.
The Fact in the Fiction
The Doom in the Gloom
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 apartment but Brennan and Booth are not convinced that he will actually move out.
The Blood from the Stones
An undercover police officer, who was investigating a string of ATM robberies, turns up dead in a van with a bag of diamonds found inside his mutilated body. So the Jeffersonian team must figure out whether or not the ATM robbers are also murderers, or if the cop was crooked. Meanwhile, Brennan is the subject of a documentary commissioned to raise funds for the Jeffersonian, and she struggles to be likeable on camera.
The Maiden in the Mushrooms
The Jeffersonian team investigates the murder of a TV producer. Meanwhile, Brennan has trouble accepting the fact that Christine might be an "average" child, when her daughter gets accused of biting another classmate. Then, Hodgins uses all of his tools at the Jeffersonian to chemically recreate Finn's special hot sauce.
The Party in the Pants
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.
The Pathos in the Pathogens
The Jeffersonian team rushes to prevent a viral outbreak while investigating the murder of journalist Mia Garrett after her infected body is found at a biohazard facility. When the mutated virus that killed Mia infects Jeffersonian intern Arastoo Vaziri, their only chance of saving him is by solving the murder. Tension and passion build as the team races against the clock to find the killer and the cure
The Secret in the Siege
Pelant returns to mess with the Jeffersonian team once again.
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