Booth and Brennan are called to the scene where a man’s body was found gutted, burned, and hung like a scarecrow on the roof of a Federal Building. Evidence left on the body re-opens a 30-year-old case and links back to Brennan’s father. Meanwhile, Zack must defend his dissertation to obtain his doctorate, asking help from a colleague.
Booth and Brennan are ordered to the cell of serial killer Howard Epps to identify the remains of an inmate. To their surprise the charred remains don’t belong to Epps. It’s soon learned that Epps has escaped and is on a revenge path, which involves Booth’s young son, Parker. Due to the danger of the case, Brennan must get FBI protection. Cam inhales a toxin while performing an autopsy, which puts her life in danger.
Brennan has to work with another agent, Agent Sullivan, while Booth needs to see a therapist. They investigate the death of a college freshman, who took part in a ‘Girls Gone Wild’ type of video and whose body is found in an alligator. Sullivan asks Brennan out.
Booth and Brennan investigate the death of Terence Bancroft, one of the Jeffersonian’s major donors, found dead at home. Hodgins compromises the case and the reputation of the lab when he removes some evidence that would link him to the Bancroft family and the case itself. Due to this, Brennan must make an important decision about her team. Booth, although cleared by Dr. Wyatt to use his gun, must continue to meet with him.
Brennan and Booth have to solve three cases that are all highly similar to those in Brennan’s new book on the bestseller list.
The team investigates the death of an Asian woman without any bones left in her body. Sully proposes something to Brennan that she does not expect.
A water main bursts in the middle of a cemetery, leaving coffins littering the grounds. Brennan is called in to identify the remains so they can be reburied. When she finds the remains, she discovers that some have only been there for five days, even though she was told that no one was buried there for fifty years. Meanwhile, Booth decides to bring Brennan in to see his shrink so that they can work on getting their relationship back on track. Also, things get intense between Hodgins and Angela when Hodgins makes a bold move.
Booth and Brennan investigate the case of a partial skeleton found in cement. Booth thinks a member of a crime family - Hugh Kennedy - is to blame, but when he hears word that Hugh was burnt to death in a car things get more complicated. Booth finds out that Hugh is actually alive, but then gets kidnapped by him. Brennan must now find Booth before he is hurt, but this is harder to do than she thinks, and she ends up going to great lengths to get Booth back safely.
A mysterious dead man is found in a crater with his body flattened as if he had fallen from the sky. Brennan and Booth try to find out who the man was while Hodgins comes up with different conspiracy theories involving aliens. Booth and Brennan find out the man was an astronaut who was murdered, and a complicated murder case unfolds.
Glowing bones are found in an old stone house, and Brennan and Booth are called in to investigate. They find that strangely, the bones are not radioactive and lack any other explanation for why they would be glowing. With the victim identified, the team sets off to figure out the murder mystery.