Months later, Brennan is still on the run from the FBI, after being framed for murder by Christopher Pelant. The remaining team searches for the real killer. They find Pelant killed the guidance counselor and proof Brennan was framed.
A burned body is found. The victim is a divorce lawyer who had a lot of disgruntled clients. With Brennan back home, she and Booth have to adjust to living together. They have various disagreements about the new routines at home.
A man dies in a car explosion. After identifying the man, Booth and Brennan find he is still alive. Turns out, the two guys are twins who did not know of the other. Both men are browbeaten by their wives, one of which wanted her husband dead.
The team identify a woman's eviscerated body as a co-owner of a natural applesauce store. There is a symmetry to her incisions. Sweets has been living in his office since the breakup with Daisy so Bones invites him to stay with he and Bones.
Brennan, intrigued by Phil Jackson's management style, pulls all her interns together as a team for a project worthy of the basketball coach's philosophy. She charges them with identifying remains that have been determined unidentifiable. For the team, however, it turns out that naming the bodies may be the easiest part of their task when one of them is from 9/11 and they must decide if he is a victim or perpetrator.
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.
An artist gluing his artwork on a billboard slips and falls with his glue on top of a corpse. The team has to separate the artist from the bones. Angela realizes the artist is a famous street painter. Bones takes up comedy to find suspects.
An archaeologist is found murdered. His lab holds ancient remains of Neanderthals and Homosapiens; these are given to Clark to research. Brennan is jealous that she has to work the current case and not the ancient one.
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 ...
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 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 dismembered body of a roller derby skater means Angela goes undercover at the rink to find more clues to the woman's murder. Elsewhere, Cam worries over the sheer number of doctor appointments Booth is going to, and presses him for details.
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 ...
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 ...
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 (guest star Luke Kleintank) 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.