Episode 1: Pilot

Episode 2: The Man in the S.U.V.

Bones and Booth find themselves on the trail of a terrorist after an SUV explodes killing the Middle Eastern man inside

Episode 3: The Boy in the Tree

When a boy is found hanging from a tree at an expensive private school all is not as it seems when this suspected suicide turns into a web of lies and scandal which stretches throughout the staff and students.

Episode 4: The Man in the Bear

When a human arm is found in a black bears stomach, Brennan and Booth travel to Washington uncovering lies and dark arts are in practice.

Episode 5: A Boy In a Bush

Agent Booth asks for Brennan's help when a Charlie, a six-year-old boy goes missing from a local park.

Episode 6: The Man in the Wall

When Bones and Angela get involved in a fight at a nightclub, Bones discovers the mummified body of a DJ in the wall with a drug stash.

Episode 7: A Man on Death Row

A death row inmate seeks Booth's help in proving he is innocent in the murder of a teenage girl. Booth enlists Bones and the gang to help decipher the truth before a possibly innocent man is executed.

Episode 8: The Girl in the Fridge

Booth asks for Bones's help when the body of a young girl is found in a refrigerator, and old emotions resurface as Bones's old professor and ex-lover visits.

Episode 9: The Man in the Fallout Shelter

It's Christmas time and Booth delivers the remains of a man found in a fallout shelter. In the examination process Zack inadvertantly releases spores of a deadly fungus meaning the entire gang have to be quarantined over Christmas.

Episode 10: The Woman at the Airport

The identification of a body found near L.A International Airport is hampered by extensive cosmetic surgery the victim had done.

Episode 11: The Woman in the Car

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.

Episode 12: The Superhero in the Alley

Brennan and Booth investigate the origins of a decomposed body that's been found in a local alley and determine it's the remains of a friendless teen.

Episode 13: The Woman in the Garden

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 use to work.

Episode 14: The Man on the Fairway

Brennan and Zach investigate a small jet crash that was carrying some Chinese diplomats and a women. 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.

Episode 15: Two Bodies in the Lab

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.

Episode 16:The Woman in the Tunnel

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.

Episode 17: The Skull in the Desert

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. The investigation leads the team to a counterfeiting ring setup in the desert.

Episode 18: The Man with the Bone

Booth and Brennan investigate a site where there might be pirate treasure.

Episode 19: The Man in the Morgue

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.

Episode 20: The Graft in the Girl

The team helps Deputy Director Sam Cullen's daughter, Laura, 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.

Episode 21: The Soldier on the Grave

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.

Episode 22: The Woman in Limbo

When the bones of a woman turn out to be Temperance's mother who disappeared 15 years ago, Temperance uncovers family secrets and has to deal with a past that haunts her.