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.
Booth and Brennan investigate a death due to an explosion in a hotel. Things get complicated when the main suspect of the investigation appears to be protected by diplomatic immunity.
The team investigates the death of a 9-year-old beauty pageant star. The girl’s competitors’ parents and siblings soon become possible suspects. Brennan makes a huge mistake when she and Booth visit a tap dancing class where they expect to find info on the killer. Back at the lab, Hodgins and Angela go on a date that actually goes well, despite what everyone else predicted.
When the skeletal remains of a federal prosecutor who disappeared five years earlier are found in the desert outside Las Vegas, the team suspects it to be tied to the mob. They then find the body of a woman a few yards away, who they suspect was killed by the same person. The woman’s injuries lead Brennan to believe she had a long history of domestic violence. When the husband denies having hurt his wife, they are led to a Vegas loan shark, where an anonymous lead takes them to the world of gambling and underground ultimate fighting, where Booth and Brennan go undercover as Vegas high-rollers. In an attempt to uncover the mystery, Booth risks his life.
The bodies of twin teenage boys, kidnapped five years earlier, are discovered. Booth and Brennan follow the trail of a notorious serial killer, known as the Grave Digger. His M.O. is to kidnap and bury his victims, then ask for a ransom. If the ransom isn’t followed, the victims are left to die. During the investigation, Brennan and a fellow colleague become the latest victims. They are forced to solve their own kidnapping from an underground grave.
While investigating the death of a film student who was working on a documentary about the legend of a headless witch, who haunted woods in the 1700’s, Brennan develops a strong bond with the victim’s brother.