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.
Bones reluctantly searches for a replacement for Zack. A skull is tossed off a highway overpass and hits a vehicle. There is evidence the victim was eaten by a cannibal.
The discovery of two mummified girls has Booth and Bones checking a fun house, a Halloween maze and a church charity for clues that may lead them to a missing girl whose parents believe she's dead.
The Gormogon killer strikes again, and his next play is a little close to home. Russ returns to face a parole violation when his girlfriend's daughter takes a turn for the worse.
Brennan and Booth investigate the death of a Santa as Bones tries to give her father the Christmas he's always dreamed of, and Booth comes to terms with not spending the holiday with Parker.