Booth’s Brother Jared Booth and Brennan investigate the scene where a body was uncovered during a botched practice police raid. The team identifies the body as a struggling inventor’s father who had recently reunited with his son. But when a second body surfaces, the team is led on a trail of deception to find out who was the actual con-man in the inventor’s life. Clark Edison returns to the lab, and he and Hodgins work on piecing together blueprints from one of the inventor’s potentially valuable inventions.

Meanwhile, Brennan likes Booth's brother and goes out on a date with him. She learns a thing or too about Booth's past while out on the date.

While trapped and trying to escape from a ship in the middle of the ocean, Booth is haunted by strange hallucinations.

When a human body is found inside the strung up Otter mascot uniform of a rival school, Brennan and Booth investigate whether the body inside the costume was dead beforehand, or killed during a Middlesex University bonfire event. The body is identified as Jimmy “Beaver” Bouvier, a fraternity brother at Middlesex University. When Brennan and Booth question his fraternity brothers, they learn that Beaver had a money-making operation on the side and was making a killing of his own. Meanwhile, Booth offers to help his brother Jared find a new job after being dishonorably discharged from the Navy.

In the season finale, a dead body is found at a club called "The Lab." The team has to do some unexpected and unusual things that have to do with this club. Brennan and Booth may become a couple.

When a human skeleton is discovered in the trenches of an old Civil War battleground, Brennan and Booth are called to the case. Despite the historical location, Brennan quickly identifies the bones as belonging to Dan Pinard, a present-day local dentist. While Booth investigates suspects, including the victim’s former boyfriend, Hodgins and lab intern Vincent Nigel-Murray work doggedly to clean the bones of a stubborn clay residue which is preventing the team from determining a cause of death. Meanwhile, Booth’s brother, Jared, returns from his travels with some suprising news.