A Boston mob boss plants a mole in the police department, while the police infiltrate the mob with their own, and both moles are in danger of being exposed.
A young man grows up on the streets following his father's sudden murder, but a chance encounter involving a mythical sword changes the path of his destiny.
When a former foster child is the chief suspect in her boyfriend's murder, Brennan tries not to take her team's criticisms of the foster system personally.
The skeletal remains of a young girl points to a serial killer that has been on death row for years, raising fears that he may have an accomplice at large.
Brennan and Booth go undercover as highrollers after a pair of bodies, belonging to a federal prosecutor and an abused woman, are dug up near Las Vegas.
Booth and the remaining Jeffersonian team try to solve the kidnapping of Brennan and Dr. Hodgins who have been buried alive before they run out of air.
Brennan's long-lost father sends her a message insisting that she drop the case of a gutted and burned mob snitch that was found on the roof of a building.
Major donors to the Jeffersonian call Booth and Brennan onto the scene when a family member is found murdered; Booth is given permission to carry his weapon.
Brennan is reluctant to interrupt her vacation to help Booth and the Jeffersonian team investigate a woman who was found without any bones in her body.
While the team investigates a suspicious body in a church graveyard, Booth insists that Brennan join him in a counseling session with his unorthodox therapist.