Brennan and Booth are called to the scene where a dead man has been found in a crater. The investigation leads them to the National Space Agency.

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.

The pieces of a dismembered body are found lying in a purple pool of water, except the head is missing. The team finds that the body belongs to Jared Addison, a science fiction writer who had several mental problems. With Sweets' help, several suspects are hunted down, however the team has trouble finding enough evidence with the victim's head still missing.

Brennan and Booth are called to investigate what appears to be charred human remains on an electrical fence. The mysterious corpse is later determined to be a mummified Egyptian royal on loan to the Jeffersonian. The anthropological mystery has Brennan in a tizzy, and when the Jeffersonian curator prepping the mummy for exhibition is murdered, the team suspects foul play. Brennan’s investigation of the curator sheds new light on the life of the Egyptian royal, turning their case into one of historic proportions. Meanwhile, Brennan goes on a date with Booth’s supervisor and former intern, and Sweets’ girlfriend Daisy Wick (guest star Gallo) returns to the Jeffersonian.

After the skull of a promising young dancer is found lodged in concrete at a construction site, the team must first figure out what happened to the victim’s skeletal structure. After learning the victim quit ballet to pursue hip hop, Booth and Brennan uncover another layer of evidence that points them to a suspect who had a secret relationship with the victim. Meanwhile, when Hannah is put on assignment in a dodgy part of town, her safety is jeopardized and her life is put in critical danger.

The team discovers the remains of a so-called "storm chaser" who seems to have died while following a tornado. But footage recorded during the storm ultimately leads them to believe he was murdered. Meanwhile, Booth becomes increasingly overprotective of Brennan both at home and in the field, and sleep-deprived Angela and Hodgins come to terms with having Angela's father and rock musician babysit their infant son.

When a corpse is found at a landfill, dyed in a blue substance, intern Arastoo Vaziri discovers a method that helps eliminate postmortem damages to the corpse, which leads the team back to a hair salon where the victim worked. Meanwhile Bones is feeling uncomfortable in her post-baby body, so Booth decides to do something special to boost her self-confidence.

The team investigates the murder of a well-known archaeologist with a questionable reputation, who came upon a career-defining discovery right before his death.

The Jeffersonian team investigates the murder of a TV producer. Meanwhile, Brennan has trouble accepting the fact that Christine might be an "average" child, when her daughter gets accused of biting another classmate. Then, Hodgins uses all of his tools at the Jeffersonian to chemically recreate Finn's special hot sauce.

The team investigates the murder of an escape artist whose body is found in the woods. They discover that the victim worked at the Magic Palace, and had some secret activities in the works that might have made him enemies in the magic community. Meanwhile, Brennan and Booth poll their friends as to whether or not the tooth fairy should visit Christine, and Angela continues to work with Sebastian Kohl on her photography.