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There is no Next Episode of Bones planned.
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 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.
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 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.
When 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 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.
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 Jeffersonian team investigates the death of a young boy whose soul remains very much alive. When psychic Avalon Harmonia attempts to help the deceased's spirit cross over, each member of the team begins to question his or her own beliefs about life after death.
The Jeffersonian team investigates the death of a professional ballroom dancer named Katarina who was murdered three days before her audition on a popular dancing competition show, "Dance to the Top." In order to solve the case, Brennan and Booth go undercover as dance competitors to observe the competition from the inside and see if they can find any potential suspects. Meanwhile, Angela struggles to balance work, family and her love for art
The Jeffersonian team investigates the death of a well-known archeologist named James Sutton, who had a questionable reputation since a lot of the work he published included false information. However, right before his death, he came across one of the greatest discoveries regarding human DNA. Meanwhile, Brennan and Dr. Clark Edison get very competitive over Sutton's artifacts that were found as they cross paths between each of their areas of expertise
After Hodgins and Angela were drugged and woke up to a bloody corpse hanging in the canopy of their bed and flower petals around their son Michael's crib, they are forced to believe that Pelant is back for revenge against Hodgins. Although Hodgins wants to go after Pelant directly, Booth knows it's best to work within the system and not go against protocol. Meanwhile, as the Jeffersonian team investigates the corpse, they discover the victim was a Special Forces agent working for the world's biggest supplier of mercenaries, and Angela and Hodgins decide to start an investigation without the rest of the Jeffersonian team for the sake of their family.
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.
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.
When Brennan is shot while working late at the Jeffersonian lab, she is rushed to the hospital in critical condition. While at the hospital, she struggles with visions of her mother that defy her usual logic. Meanwhile all evidence suggests that Brennan's attacker may be linked to the Jeffersonian.
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.
When extremely educated new intern Dr. Oliver Wells 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 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.
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.
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 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 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 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 -.
When evil tech genius Christopher Pelant returns to toy with the Jeffersonian team in their newest investigation, they discover that the string of murders that have been occurring are tied to FBI agents close to Booth. Meanwhile, as the investigation unfolds, Sweets realizes that the evidence seems all too familiar to him and Brennan starts evaluating her relationship with Booth when signs begin to point to him as a potential target of Pelant's.