Forensic anthropologist Temperance "Bones" Brennan and her team work with the FBI to solve murders by identifying victims from their remains in a procedural series inspired by real-life forensic anthropologist and novelist Kathy Reichs.
In the Season 9 premiere, the remains of a State Department accountant are found in a hotel's air-conditioning unit, but the investigation takes an unusual turn when Booth discovers that an old Army pal, who's now a CIA agent, is also looking for clues. Meanwhile, Booth seeks advice from a friend and former priest about his relationship with Brennan, who is uncertain about their future together.
Brennan and Booth go undercover as Roxie and Tony, respectively, at a couples retreat while investigating the death of a management consultant, whose remains were discovered being eaten by bobcats. Meanwhile, Cam's identity is stolen, which leads to her being mistakenly arrested; and Sweets mulls taking a leave from the FBI.
A gang member's remains are found in a burned-out car, and Sweets, who's taking time off from the FBI, helps out with the investigation when a boy from the neighborhood center where he's a volunteer turns out to be the son of a gang member.
A plan to catch Christopher Pelant involves using a human cadaver to stage a murder to match his style and draw him out, but he refuses to take the bait and retaliates by killing someone close to Booth. Meanwhile, Sweets returns to the FBI, but questions the team's trust in Agent Hayes Flynn.
An investigation of the murder of a high-school principal who had cancer leads to his bucket list after the discovery of a video of him punching UFC champ Chuck Liddell in the face. Meanwhile, Brennan and Booth start to plan their wedding; and Sweets learns he may be replaced by a machine.
Brennan and Booth's wedding day approaches, but details of a murder probe are kept from the bride so she can stay focused on her big day. Meanwhile, Brennan's father, Max, arouses suspicion when he shows up with a duffel bag full of money.
Brennan and Booth's honeymoon in Buenos Aires turns into a busman's holiday when they help a detective, who's a fan of Brennan's books, investigate the murder of a Nazi war criminal whose remains were found in a mass grave. Meanwhile, Angela and Hodgins have their hands full taking care of Christine while her parents are away.
The investigation of a model's murder reveals that his main source of income was sperm donations, but the discovery that he falsified records spawns a long list of suspects. Meanwhile, Brennan gets into a feud with a fellow author; and Hodgins keeps an eye on a fly larva.
Brennan serves as a juror on a case involving a professional soccer player who's charged with murdering his wife, but she doesn't think he's guilty until his best friend also winds up dead, and then it becomes a team effort to prove he's the killer.
The murder of a food scientist is investigated after human remains are mixed with cans of stew served in a school cafeteria, but when the team discover the deceased's latest invention, it leads to a trail of jealous suspects in a cutthroat industry. Meanwhile, Angela plans a post-wedding bachelorette party for Brennan that gets out of hand.
A nationally ranked gymnast is murdered and her remains are hit by lightning and strewn about a public park, and evidence suggests she was leading a double life, but Booth is more puzzled by Brennan's empathy for the victim's father. Meanwhile, Cam confronts the woman who stole her identity.
Brennan dreams about Christopher Pelant during the investigation of the death of a girl who was murdered 18 years ago, and one of the suspects turns out to be an ex-boyfriend who was also a friend of Hodgins'.
A country-music singer's remains are found in a shallow grave, and the Jeffersonian's investigation uncovers his record label's mistreatment of him. Meanwhile, Wendell breaks his arm in a hockey game, but Brennan discovers shocking news when she examines his injury.
Sweets goes undercover in the world of professional chess after a champion's body is discovered in pig slop. Meanwhile, Cam balks at being recognized by a science publication since she feels the honor should go to Brennan; and Canadian podiatrist Douglas Filmore visits the Jeffersonian to work as an intern.
A kidnap victim's remains are identified after being found in a park, and the team wonder if the deceased's strained relationship with her mother might have anything to do with her murder. Meanwhile, Hodgins learns a secret about his family; and Brennan and Booth debate commingling their funds.
The murder of a CIA informant sends Booth and CIA agent Danny Beck on the trail of an Afghan terrorist. Meanwhile, Brennan wants to spend more time in the field with Booth, but they wonder what impact it will have on their family.
The remains of a repo man are found in a septic tank, but the investigation reveals his dark past and more than a few suspects. Meanwhile, a forensic anthropologist from Cuba becomes a Jeffersonian intern after defecting; and Brennan and Booth mull whether or not their daughter should have a religious upbringing.
The investigation of the murder of a children's TV icon takes a detour when his reputation for promiscuity emerges, which leads to a long list of unlikely suspects. Meanwhile, Brennan and Booth get ready for Christine's first birthday; and intern Clark solicits opinions of a novel he's just written.
Three people's remains in a single urn confound the Jeffersonian team after a wealthy artifact collector walks into his own funeral. Meanwhile, Finn and Hodgins strike it rich with their hot-sauce venture, but Finn's enthusiasm is tempered by devastating news from Michelle.
Remains found in a log in a forest belong to an art-school dropout who had lupus, and the investigation reveals marijuana use to ease her pain, but her work at a dispensary may have had something to do with her death. Meanwhile, Wendell Bray reveals information about his illness; and Booth gets ready for his FBI competency test.
Remains found in a swamp belong to a woman who was cryogenically frozen before being discarded, which leads the investigation to a preservation facility. Meanwhile, Cam is nervous about meeting Arastoo's parents; and Booth is up for a big promotion, but it might mean relocating his family.
Remains in a national park belong to the daughter of the wealthy McNamara family, and the investigation reveals she may have been murdered by the Ghost Killer and had a connection to a previous victim. Meanwhile, the case draws interest from the FBI's deputy director.
The remains of a swim coach at a community college are found at the bottom of a well, and the investigation reveals he may have been having an affair. Meanwhile, Booth prepares to testify before a Congressional subcommittee, so his place in the current case is filled by Sweets, who is smitten with a new intern at the Jeffersonian.
In the Season 9 finale, a conspiracy blogger's death arouses suspicion when he dies before a scheduled meeting with Booth to discuss a previous case, but evidence uncovered during the team's investigation could affect his future with the FBI. Directed by series regular David Boreanaz.