The Gormogon serial killer is back again, and the silver skeleton from the basement vault has gone missing. All the Jeffersonian employees become suspects, with the scary possibility that one of their own is working with Gormogon.
A wannabe singer Tommy Sour was found on a grassy location. The investigation leads Brennan, Booth, and Cam to the Checker Box Restaurant where Tommy used to sing. There are several suspects who took part in the open mike contest there, with talent scouts in the audience. The group comes together with a startling revelation for Brennan.
Brennan's father Max Keenan is on trial for the alleged murder of FBI Deputy Director Kirby. Everyone on the team, except for Brennan, is called as a witness for the prosecution during the trial. Brennan on the other hand is the forensics advisor for the defense, and she must rely on both her dedication to her family and her skill as an anthropologist to help free her father.
A woman's car is run off the road and she is killed, but her baby miraculously survives the accident. Booth and Brennan go to the woman's hometown to try to find out who's responsible for running her car off the road. Bones, with help from Booth, takes care of the baby until the team finds out who killed the mother.
All team members are working to identify the bones from a college athlete who suffered a lot of fractures. After the body is identified they talk to his sister and somebody who acted as a sort of an adviser for the deceased. Angela and Hodgins have an important talk. Zack is overwhelmed by having to reconstruct the crushed bones to form a skeleton.
A body is discovered at Homestead Natural Hot Springs in a spring filled with mud. Booth and Brennan go to investigate the scene and find that the body is that of Tripp Goddard, a sexy motorcycle racer who had been murdered about two weeks ago after a race. Sweets' girlfriend is also introduced.
Booth and Brennan investigate a mall Santa named Kris Kringle who was found dead by two elves. A series of clues makes the murdered mall Santa seem like he's the real deal.
The body of an archbishop is found by some construction workers. The archbishop's kneecaps were surgically removed, which prompts the team to return to the Widow's Son case.
A time capsule buried by a high school class of 1987 is unearthed by a group of the school's alumni who are shocked to find the body of one of their high school classmates hidden inside. Booth and Brennan find that the victim was an outcast in high school, so they go on to investigate the past lives of the classmates in an effort to discover the murderer.
The team suspects their own colleagues after the burnt remains of an intern at the Jeffersonian are found in the building's incinerator. At first it's thought that she might have been killed because she was working on an artifact in the Widow's Son case, but then things become more complicated when romantic ties between her and another employee at the Jeffersonian surface. Meanwhile Booth poses as Cam's boyfriend on one of her family get-togethers.