When a lake gives up skeletal remains, FBI Agent Booth goes to forensic anthropologist Dr. Brennan. She eventually determines that it is the body of a former Washington aide and the investigation becomes problematic.
A driver dies in a cafe car bombing and Booth turns to Brennan for help in identifying the remains. The clues point to another potential terrorist act. Brennan catches Booth with his lady.
Though the hanging corpse of an Ambassador's son found at a private school is initially ruled a suicide, Booth and Brennan both believe that some other scenario may have played out.
A black bear in Washington is found to have a human arm in its stomach and Brennan and Booth try to find out why. Brennan finds herself sought after by all the town's men. Hodgins and Addy vie for a delivery woman.
Brennan and Booth try to find justice for a 6 year old, Charlie, who went missing and whose bones are discovered. The investigation reveals sexual assault and murder.
A fight at a club reveals a mummified body hidden in the wall with some drugs.
Booth brings Brennan in to go over the case of a man sentenced to die in less than two days. When evidence starts to point to a possible other murderer, Booth tries to keep a man he put away from being killed.
Brennan goes toe-to-toe with a former mentor over a case that involves the body of a girl discovered in a refrigerator.
Zack inadvertantly releases deadly fungal spores while cutting into a body and because Hodgins wasn't following protocol, Booth, Brennan and her staff are forced to spend the holiday in quarantine.
Booth and Brennan try to discern the identity of a female body found near LAX. The task is made more difficult by plastic surgery. While in LA, Brennan meets with Penny Marshall who has plans to adapt her books. Back in DC, Goodman leads Brennan's team in trying to decide whether an Iron Age skeleton is authentic.
The suspect in the death of a woman and abduction of her child is the child's father, but, as it turns out, he's already enrolled in the Witness Protection Program.
Brennan and Booth investigate a teenage body found wearing a superhero costume. The comic book shop leads them to a live action role-playing game. Goodman tries to learn more about the victim, Warren, through the dead teenager's comic book writing. Examination of the bones reveals that Warren was actually dying from leukemia.
The investigation into a body found in a gang member's trunk gets even more complex when Booth and Brennan trace it to the original burial location and find an empty second grave. The second body is discovered in a Senator's garden.
Brennan and Zack look into the case of a crashed plane which was housing a woman and several Chinese diplomats, but Brennan curiously discovers bone pieces of a man that don't match any of them. Though Dr. Goodman is adamant that the diplomats be the team's priority, Temperance decides to look into the man's identity.
Brennan unknowingly becomes part of a shooter's violent plan when she heads out to meet a prospective internet date at an eatery.
Brennan and Booth find the remains of a body in an underground tunnel and learn that there is a hidden society of homeless people living there.
Angela discovers a skull in the desert, but seeks Brennan's help in identifying it, fearing it could be her vanished boyfriend. The inquiry into the skull takes the team out to the desert, where a counterfeiting operation is in play.
When a dead body is found clutching a 300-year-old finger bone, Booth and Brennan's investigation leads them to a dive site off the coast of Assateague Island where a pirate treasure may be buried.
Booth is in New Orleans assisting with the identification of Katrina victims. While in New Orleans Booth learns that Brennan has been attacked and left bloody in a motel room.
A young cancer patient may be the victim of a crime. When Brennan learns of a young girl who is suffering from cancer caused by a bone craft she received for a previous condition, she decides to dig deeper into the history of the bone that was used to treat the young girl. But when Brennon discovers there are more people with the same rare terminal disease, she believes young Amy might be the victim of foul play.
Brennan and Booth go to investigate an apparent suicide in Arlington National Cemetery, but soon find out that it was murder and that the victim was a soldier who had served in Iraq. The investigation leads to a lot of unanswered questions about the military unit of the victim, with all clues pointing to a cover-up. Booth meanwhile recalls his shady past as a sniper in the military and the horrors of war.
Brennan receives some bones that she must identify, but is stunned when she finds that the remains are those of her mother. Brennan is hit hard by this discovery, and understandably so, since she never knew what happened to her parents after they disappeared 15 years ago.