An investigation into a train wreck that claimed three lives, one of them a U.S. senator. In other events, Brennan clashes with the new boss, Dr. Camille Saroyan, who has a romantic history with Booth.
Booth seeks out the husband of a missing pregnant woman after her remains wash up onshore, but the suspect disappears. Meanwhile, Bones continues to clash with Cam, and Booth gets a visit from his ex.
When a tractor-trailer collides with a garbage truck, the skeleton of a 17-year old boy is found in the trash. A facial imprint from a shroud that wrapped the body helps identify the victim as a suburban honor student.
The headless skeleton of a young man is found in a state forest. Brennan and Booth's investigation becomes entangled in the local legend of a woman who was decapitated as a witch in the 1780s and is said to still haunt the forest.
Booth and Bones investigate a murder that is connected to Bones' father. Meanwhile, after obtaining his doctorate, Zack gets a makeover to appear more professional.
After Howard Epps orchestrates an escape from his penitentiary, he starts picking off the Jeffersonian team one by one and taunting Brennan with clues to save them.
While Brennan is paired up with another FBI agent to solve the murder of a co-ed found inside an alligator in the Everglades, Booth is sent to therapy after shooting a clown-shaped speaker on an ice cream truck.
When Booth and Brennan keep butting heads in a case involving a Catholic church, he convinces her to see Dr. Wyatt with him, and Hodgins suggest a change in his and Angela's relationship.
Homeland security asks Bones to examine some remains, thinking they're radioactive, and although the site is cleared two questions remain: why was an up and coming chef murdered, and why are the bones still glowing?
As the wedding approaches, the team investigates the life/death of a little girl. Bones's father shows up, with an heirloom and a message from her mother.
