The team works to identify the bones of a college athlete who was crushed behind gym bleachers. After the body is identified as star player RJ Manning, they discover that he was murdered. Booth and Brennan follow several leads, at one point thinking there could have been multiple killers.
A woman’s car is run off the road and she is killed, but her baby miraculously survives the accident. Booth and Brennan go to the woman’s hometown to try to find out who’s responsible for running her car off the road. Bones, with help from Booth, takes care of the baby until the team finds out who killed the mother.
Brennan’s father Max Keenan is on trial for the alleged murder of FBI Deputy Director Kirby. Everyone on the team, except for Brennan, is called as a witness for the prosecution during the trial. Brennan on the other hand is the forensics advisor for the defense, and she must rely on both her dedication to her family and her skill as an anthropologist to help free her father.
A wannabe singer Tommy Sour is found in a grassy location. The investigation leads Brennan, Booth, and Cam to the restaurant where Tommy used to sing and where several suspects who took part in the open mike contest are, including a woman who was obsessed with Tommy and turns her affections towards Booth after learning of Tommy’s death. Also, something horrible happens during the investigation which shocks the Jeffersonian team.
The Gormogon serial killer is back again, and the silver skeleton from the basement vault has gone missing. All the Jeffersonian employees become suspects, with the scary possibility that one of their own is working with Gormogon.
Brennan is summonsed to a train derailment … and discovers she has a new boss. A train carrying a popular senator was derailed by a car positioned on the tracks. Brennan works out why the dead body of a rich businessman was placed in the car. Meanwhile, she continues to try to find her father.
Booth and Brennan examine the remains of a woman and fetus found in the Delaware Bay. The body is a pregnant newlywed whose mysterious disappearance one year ago had been a major national news story. Her husband is the prime suspect in the case, but he disappears before Brennan and Booth question him, prompting Booth to call for a manhunt. Booth is upset that his ex-girlfriend is letting their son spend time with her new boyfriend.
An overturned garbage truck reveals the body of a young man who’s been missing for nearly three weeks. When the investigation reveals that a young girl raised by foster parents is the chief suspect, Brennan becomes disheartened by how quickly the rest of the team lays blame on the foster care system - something she’s been through herself. Tension continues to rise between Cam and Brennan.
After digging up the skeletal remains of a young girl, it becomes clear to Booth and Brennan that they’re not dealing with a normal case. It’s confirmed at the lab, when they discover that the cause of death points to a convicted serial killer on death row who they’ve captured in a previous case. A clue is found on the body that leads to another victim - this one only a week old. Brennan and the team must decipher cryptic clues to find the serial killer’s accomplice. Things get worse when the team finds out the next victim is still alive. They have to test their limits, racing against the clock, before the young girl becomes the next victim.
There are two suspects with the same motive when Booth and Brennan investigate the murder of a man found in a bathtub full of chemicals. They soon discover that he had two wives and a girlfriend.