When a woman’s burned body is found in a car with signs that her child was kidnapped, Brennan and Booth suspect the father, Carl Decker. But things get complicated when Decker turns out to be in the witness protection program.

Brennan and Booth investigate the origins of a decomposed body that’s been found in a local alley fully dressed in an unorthodox costume. They determine it’s the remains of a reclusive teen that they discover has a secret second life.

Booth and Brennan are called in to investigate when a dug up corpse is found in the back of a gang member’s car. While he is being questioned, a drive-by shooting allows him to escape. Booth and Brennan follow the clues, which lead them to another empty grave as well as a wealthy senator’s house, where the gang member used to work.

Brennan and Zack investigate a small jet crash that was carrying some Chinese diplomats and a woman. At the crash site, Brennan finds some bone fragments that do not belong to any of the passengers, but might belong to a man who has been missing for five years. Dr. Goodman orders the team to work solely on the Chinese diplomat case, but Brennan decides to go behind his back to investigate the bone fragments.

When Brennan decides to give on-line dating a try she ends up the target of a shooting at the local restaurant where she’s meeting a date. The resulting investigation reveals that the shooter could be connected to any one of the two cases that she is working on. She ends up getting somebody hurt and is leaning towards danger herself when her shooter comes after her.

Brennan and Booth stumble upon a subterranean world of homeless people when they find the remains of a filmmaker in the ventilation shaft of an underground tunnel.

While on vacation, Angela finds a skull in the desert. She asks Brennan for help in identifying the skull because she is afraid it might be her boyfriend, who has gone missing with a local guide. The investigation leads the team through a violent boyfriend, the local sheriff and ultimately to a counterfeiting ring setup in the desert.

Booth and Brennan investigate a case involving a 300-year-old finger bone and a site where there might be pirate treasure. Hodgins is excited when he’s able to leave the lab and help with the case, but his life is put in danger and it’s up to Booth and Brennan to save him.

Brennan takes a vacation down to New Orleans to help identify victims of Hurricane Katrina. While at her hotel, she wakes up the next morning bloody and beaten, with no memory of what happened. Booth comes down to try and help her figure out what happened. When the local medical examiner is found murdered, Brennan becomes the suspect. Their investigation leads them into the world of voodoo.

The team helps Deputy Director Sam Cullen’s daughter, Amy, when she contracts a rare form of lung cancer after receiving a bone graft. Booth and Brennan learn she is not the only victim with this rare form of cancer.