A train carrying a popular Senator is derailed by a car positioned on the tracks. Brennan works out why the dead body of a rich businessman was placed in the car, and the search continues for her father. The team has a new boss.
When the remains of a young pregnant woman and fetus are found in the Delaware Bay and identified as a newlywed who disappeared a year earlier, the investigation is aimed toward her husband, but takes a surprising turn. Booth is upset that his ex-girlfriend is letting their son spend time with her new boyfriend.
When the body of a young man, who's been missing for nearly three weeks, is discovered, the investigation leads them to his girlfriend, who is a foster child. Bones becomes emotionally involved in the case since, she too, became a foster child after her parents disappeared.
After digging up the skeletal remains of a young girl, the investigation points to a convicted serial killer on death row. The team follows cryptic clues that lead to another body, an accomplice, and a victim who may still be alive.
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.
The team investigates the death of a 10-year-old beauty pageant star. The other contestants, their parents, and their siblings all become possible suspects. 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. Booth and Brennan go undercover as Vegas high-rollers in an attempt to uncover the mystery, Booth risks his life.
The bodies of twin boys, kidnapped five years earlier, are discovered. The investigation lead Booth and Brennan to a notorious kidnapper known as the Grave Digger. During the investigation, Brennan and Hodgins become the Grave Digger's next victims.
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.
Booth and Brennan are called to the scene where a man's body was found hung like a scarecrow, gutted, and burned on the roof of a building used by the FBI to hide witnesses.
The notorious serial killer, Howard Epps, sets his prison cell on fire as part of a daring prison escape. Brennan is his target and her entire team is placed in danger.
Brennan has to work with another agent while Booth needs to see a therapist. The duo investigate the death of a college freshman, who took part in a 'Girls Gone Wild' type of video.
Booth and Brennan investigate the death of Terence Bancroft, one of the Jeffersonian's major donors, found dead at his home. Hodgins' relationship with the wife of the deceased years earlier, compromises the case.
A broken water main uproots multiple coffins in an old graveyard. When the team is brought in to identify the bodies for re-interment, they discover a newer skeleton that should not be in the graveyard, which has not been used for 50 years.
When Angela draws the face of an old woman to go with the decomposed skeleton of someone much younger, they soon learn the victim had Progeria, an aging disease. Booth and Brennan investigate to discover who would want to kill such a fragile person. Meanwhile, Hodgins and Angela's walk down the aisle doesn't go as planned.