Brennan and the Jeffersonian team are desperately working to get Booth out of jail, clear his name and absolve him of crimes he did not commit. The remains of a man who has been dead 16 years could be the point of origin in the entire government conspiracy that ultimately put Booth in jail. Meanwhile, Booth is faced with a challenge from a new and politically ambitious FBI agent. As he awaits trial, Booth also realizes that many of the convicts with whom he is locked up are criminals he put in there, and Daisy and Sweets have a surprise for the rest of the Jeffersonian team.

To find out who framed Booth for murder, the Jeffersonian team, with the help Special Agent James Aubrey, continues to investigate who is behind a conspiracy within the Federal Government that dates all the way back to J. Edgar Hoover. Then, when foreign DNA is found in a previous victim linked to the scandal, the team is able to narrow down the number of suspects, leading them closer to cracking the case.

With the help of "squintern" Rodolfo Fuentes , the Jeffersonian team investigates the murder of a controversial conservative radio host whose remains were found in a storm drain. When the team discovers some of his extracurricular activities, they come across shocking evidence that narrows down the suspects. Meanwhile, Special Agent James Aubrey is desperate to gain the trust of Booth, and Brennan is worried about Booth's psychological well-being after recent events.

The Jeffersonian team, with the help Special Agent James Aubrey, investigate the murder of a video game designer whose remains were found washed up in a river. When the team uncovers more about the fortune the victim had acquired throughout his career, everyone who was close to him becomes a suspect. However, the investigation takes a turn when they discover that the victim was playing his own games on people. Meanwhile, "squintern" Jessica Warren enlightens the team about the educational cooperative with which she has been involved and Brennan and Booth discuss Christine's future.

The Jeffersonian team attends a forensic science convention with Brennan delivering the keynote speech, only to discover the remains of a body in a stairwell at the convention. With numerous convention attendees offering help and their products, evidence points to Dr. Hodgins as a suspect and the team has to find a way to prove his innocence. Meanwhile, Brennan runs into her publishing rival, Tess Brown and "squintern" Wendell Bray has news about his cancer diagnosis and returns to work with Jeffersonian team.

The Jeffersonian team investigates the murder of an immigrant maid whose remains were found on the side of the road. The victim's wealthy former employer, Sandra Zins, is a key suspect in the case, but when the team discovers that the victim might have been brought into the country illegally, the team realizes the case is much bigger than it seemed. Amidst talks of marriage between Cam and "squintern" Arastoo, tensions rise between Brennan and Cam as Arastoo prepares his dissertation for Brennan's approval.

After severely damaged human remains are discovered under a merry-go-round, the Jeffersonian team begins a complicated investigation of a billion dollar hedge fund company. When the victim's boss (guest star Gill Bellows) becomes a prime suspect in the investigation, the case takes a major turn as the team uncovers incriminating evidence against the victim. Meanwhile, the investigation becomes increasingly difficult as Aubrey feels an emotional connection to the case, and Booth and Brennan are at odds when Christine curses for the first time.

After a famous crossword puzzle master is found in an urban fracking site, the Jeffersonian team investigates puzzle champ's fellow players in order to track down the killer. After discovering that the victim was suffering from a mental illness when he died, the team realizes the case is much more complicated than it seemed. Meanwhile, a very pregnant Daisy (guest star Carla Gallo) seeks comfort from her doula, Valentina (guest star Mindy Cohn), and the newest member of the Jeffersonian family arrives.

When the Jeffersonian team investigates the remains of a college psychology professor, the victim's controversial social experiments on his grad students garners a list of highly motivated suspects. Meanwhile, Booth is sidelined with online traffic school, causing Brennan to team up with Aubrey, and Wendell struggles with his feelings towards a chemotherapy treatment nurse.

BONES pays homage to Alfred Hitchcock in an episode that reimagines the Jeffersonian and FBI teams in 1950s Hollywood. Brennan plays an LAPD detective who's battling sexism on the force, and Booth is a notorious jewel thief who is far more than he seems to be. When Booth is framed for the murder of a rich socialite, he and Brennan team up to clear his name and find the true identity of the murderer.

The Jeffersonian team, with the help of Angela’s psychic friend, Avalon Harmonia (guest star Cyndi Lauper), is drawn into the twisted world of fortune tellers when the body of a local psychic is found decomposing in the trunk of a tree. However, when the team learns more about the victim’s personal life, those closest to her become suspects. Meanwhile, Booth and Brennan debate the pros and cons of Christine’s new imaginary friend and the team remembers Sweets on his birthday.

When an affluent school teacher is found dead in an abandoned bookstore, the teachers and students at her school become suspects in the case. Meanwhile, Brennan’s publisher encourages her to join Twitter to help grow her fan base, and “squintern” Jessica Warren (guest star Laura Spencer) teaches Brennan some tricks to master the Twitter-verse, skills Brennan enthusiastically puts to use.

When the body of an ex-con is found in pieces, the Jeffersonian team investigates a local bakery known for employing former felons. But they soon learn that the victim was involved in a robbery gone bad, and start targeting suspects from the ex-con’s past. Meanwhile, “squintern” Arastoo Vazirir (guest star Pej Vahdat) must decide whether to return to Iran to visit his dying brother, which causes friction between him and Cam.

The Jeffersonian team unravels an unexpectedly competitive world of mini-golf as they try to figure out the murder of the sport’s superstar. Meanwhile, Brennan is worried her father Max is reverting to his criminal tendencies and “squintern” Wendell Bray enlists Hodgins to help him fix his girlfriend’s family heirloom

When the remains of a high-stakes gambler are found in an industrial shredder, Booth risks relapsing into his gambling addiction as he and Brennan delve into the world of underground poker. Meanwhile, Hodgins invents a new product related to the lab, and Brennan and Booth find out some exciting news.

The body of a popular TV celebrity chef are discovered at a local park, and the Jeffersonian team must search for clues in local restaurants that he had been reviewing. When evidence points to the Royal Diner, Brennan and Booth’s favorite eatery, the two must risk their status as favored patrons by questioning the staff. Meanwhile, Hodgins sells his new invention for millions and Brennan creates an anatomically correct song to help Christine learn about the bones in the human body.

When the remains of a private high school student are discovered in a ditch, Brennan and Booth surmise that bullying was a factor. When Brennan discovers similarities between her own teen years and the victim’s, it leads the team to question whether or not the girl’s death was, in fact, a murder.

With only 48 hours before the execution of serial killer Alex Rockwell, whom Brennan and Booth helped convict, the Jeffersonian team must race against the clock to confirm Brennan’s new suspicion that Rockwell may not have been responsible for those crimes.

When a powerful member of the Iranian parliament kidnaps Arastoo (guest star Pej Vahdat) to have him aid in a murder case, Booth and Cam head to Iran, and the rest of the Jeffersonian team must race against the clock to help expose the killer. Meanwhile, Brennan discovers the truth about Booth’s growing gambling habit, and she turns to Aubrey for help to keep her and Christine safe from her husband’s menacing bookie.

When the body of a well-known cookie jar collector is found in a riverbank, the Jeffersonian team must submerge themselves into the victim's collector community in order to catch the murderer. Meanwhile, Booth struggles to come to terms with Brennan's decision that he move out of their house due to his gambling addiction and Aubrey has his eye on one of the "squinterns".

When the remains of an ex-con and biker gang member-turned-yoga instructor is found in the aftermath of a forest fire, the team must navigate both worlds from the victim’s past to find the killer. Meanwhile, Booth continues working hard to beat his gambling addiction and regain Brennan's trust, and Angela and Hodgins make a big decision that will impact their future at the Jeffersonian.

When the Jeffersonian team discovers remains of a victim, and elements of the crime scene point to a possible protege of serial killer Christopher Pelant, they must revisit their prior work on Pelant while tracing new clues that will hopefully lead them to the copycat killer. Meanwhile, Angela is skeptical about her and Hodgins decision to move to Paris and Brennan and Booth contemplate options outside of the Jeffersonian and FBI.