Booth and Brennan go to investigate a body found in the Chesapeake Bay. After arriving, they find only the upper torso, giving the team little to work with other than remnants of the victim's breast implants. Brennan and Booth are led to a small church in Maryland, where they find that the victim was a pastor. When the team finds the lower half of the body, they learn that their initial assumptions may not been incorrect.

A shallow grave holds the remains of conjoined twins; Booth and Brennan infiltrate a circus community after they discover that the twins were jugglers there.

When newlyweds encounter a corpse while bungee-jumping off of a bridge, Brennan and Booth are sent to investigate. After determine the cause of death was not suicide, the team at the Jeffersonian discover an unknown substance coming from the body. This sends the lab into lockdown and have only 24 hours to uncover the murderer before the body disintegrates.

Booth and Brennan are sent to investigate when human remains are found during a photo shoot. When the team uncovers a meteorite in the victim's ear, they are led to the Collar Institute of Science in D.C.

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.

Stephen Fry returns as Dr. Gordon Wyatt. Booth, still suffering some lingering effects from his brain surgery, has to get re-certified for FBI marksmanship, but is not the accurate shot he was before going under the knife. He and Brennan investigate the death of a little person who was a former wrestling star.

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.

An event for a candymaker (Wayne Knight) turns bitter when human remains are discovered in the world's largest chocolate bar; Cam struggles with her daughter's decision to attend a college that fails to meet her high standards.

Sniper Jacob Broadsky takes out a victim who escaped from the justice system; Booth uses his military training to try to stop Broadsky before he strikes again; Angela's father visits the Jeffersonian.

The remains of a mythbuster television show host are found in the wilderness appearing to have been killed by the mythic Chupacabra, a reptile-mammal hybrid creature whose existence has not been confirmed. The team soon learns that the victim traveled to the remote West Virginian area to debunk the Chupacabra myth, and they interrogate possible suspects, including a rival wilderness-channel host/cryptozoologist/pet psychic. But when a tape is recovered at the crime scene and peculiar tooth marks are found in the victim's remains, the team learns details about the victim's demise that challenge the original theories surrounding his death. Meanwhile, recovering alcoholic squint Vincent Nigel-Murray makes amends with each member of the team and makes some surprising confessions.

Rogue sniper Jacob Broadsky returns once again, claiming another victim and making Booth determined to put him away once and for all.