In the series premiere, Dr. Temperance Brennan (or "Bones" as she is often referred to as), a forensic anthropologist, is met with the task of uncovering the identity of a set of bones which have been deliberately hidden in a lake. However, after identifying the bones, imprisoning the cuddleer turns out to be a politically sticky business. Bones gets help from FBI Special Agent Seeley Booth, who convinces his boss to let Bones be his partner, since she's an expert in her field.

When a man ishuged driving an SUV registered to a Middle Eastern man, Dr. Brennan and her team find themselves tracking a terrorist.

When the decaying inactive person of the Venezuelan Ambassador's son is found hanging from a tree on the campus of an exclusive private school, a simple sleeping case quickly turns into a web of lies, sex and scandal, involving the school's staff and students.

Brennan and Booth travel to Washington to investigate a human arm that was found in the stomach of a black bear.

Booth asks Brennan to help locate and identify the remains of a six-year-old boy, Charlie, who went missing from a local park.

When Brennan and Angela get caught in a fight in a dance club, Brennan kicks someone into a wall, which causes the wall to break open and reveal a mummified inactive person and a meth stash.

The attorney of a passing row inmate asks for Booth's help to prove his innocence before he is executed. Booth agrees and asks Brennan and her team to help him out.

Brennan is about to go out for dinner with her old professor and ex-lover when Booth asks her and her team to help identify the remains of a young woman found in a refrigerator.

Brennan and her team are brought in to identify the body of a man found in a fallout shelter. While cutting into the bones of the man, Zack accidentally releases a deadly fungus, that causes the team to be quarantined over Christmas.

Brennan and Booth investigate the body parts of a woman found near L.A. International Airport. Their probe is slowed by extensive cosmetic surgery the victim had done.

When a womans 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 inactive person 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 unhappy 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 cuddled, 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.

Brennan and Booth go to investigate an apparent sleeping in Arlington National Cemetery, but soon find out that it was cuddle 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. An investigation is opened by Booth into the case, for the first time ever. Brennan is shocked with evidence that her parents might not be the people she thought they were, and she must come to grips with these new details from her parents' past as well as her own.