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From executive producers Barry Josephson and Hart Hanson comes BONES, an investigative drama inspired by real-life forensic anthropologist and best-selling novelist Kathy Reichs. Dr. Temperance Brennan is a highly skilled forensic anthropologist in Washington, DC. FBI Agent Seeley Booth calls on her to assist with investigations when the standard methods of identifying a body are useless - when the remains are badly decomposed, burned or destroyed beyond recognition. In the season premiere, Booth asks Brennan to help provide clues and information when skeletal remains are found at the bottom of a lake. With her team of specialists at the Jeffersonian Institute, Brennan determines the identity of the remains to be the ex-aide of a Washington, DC, congressman. A series of clues add up to murder, and Brennan wants in on the case. Although skeptical of all scientists, or "squints" as he calls them, Booth knows if he wants Brennan's expertise on the case, he's going to have to give in to her demand to a partnership with him and let her out of the lab. But Brennan may have gotten more than she bargained for when she digs under the surface to uncover who was behind the murder.

Car bomb explodes in front of a busy café, killing the driver and a number of the cafés patrons, and injuring others. Since the car was registered to a prominent Middle Eastern man with U.S. government ties, Agent Booth calls Dr. Brennan into the case to help with the identification of the driver. Once the driver's identity is revealed, Brennan and Booth uncover clues that lead them in an unexpected direction - on the trail of a terrorist before another murder is committed. Meanwhile, Brennan and her team discover that Booth is seeing a woman, which inspires Angela to look further into Booth's personal life in hopes of convincing Brennan that she has a chance for romance with Booth.

When the decaying corpse of the Venezuelan Ambassador's son is found hanging from a tree on the campus of an exclusive private school, Dr. Temperance Brennan and Agent Seeley Booth are called in to investigate. The cause of death seems to be suicide, but both Brennan and Booth suspect there may be an alternative cause of death. As Brennan partners with Booth on the case, Booth isn't entirely comfortable with the rest of Brennan's team's out-of-the-lab mingling with him. As Brennan and her team at the Jeffersonian Institute dig deeper into the possibilities of how the Ambassador's son died, Booth and Brennan uncover the killer as well as a web of sex, lies and scandal involving the school's staff, students and parents.

When a human arm is found inside the stomach of a black bear, Brennan and Booth travel to Washington state to investigate. They search a small town for clues and discover that ritualistic cannibalism is involved. After a symbol points to the suspect's occupation, Brennan and Booth realize that there is sometimes more to an autopsy than they thought .

Brennan, working hard on her latest novel, is enlisted by Booth to help locate and identify the remains of Charlie, a 6-year-old who went missing from a local park. Brennan determines that Charlie was sexually assaulted before he was murdered, which leads Booth to conclude they're on the hunt for a serial pedophile. When the prime suspect is eliminated, Booth and Brennan pay a heartbreaking visit to Charlie's mother, Margaret, to inform her that Charlie's killer is still on the loose. Suspicion creates uncertainty - among even the people closest to Charlie - and Brennan and Booth must investigate all leads, no matter whom the information points to.

When Brennan and Angela get caught in a melee in a dance club, Brennan kicks someone into a wall, causing it to break open and revealing a mummified corpse and a stash of methamphetamine. Once it's determined a murder was committed, Brennan and Booth pair up to follow a trail of drugs and money within the Washington, DC, club scene. Their investigation uncovers a turf war between artists within the local urban music industry, where the quest for success may end in death. Meanwhile, it remains to be seen if Booth's current relationship is ready to move to the next level.

Condemned man Howard Epps is scheduled to be executed by lethal injection in 32 hours for the murder of 17-year-old April Wright. Epps' attorney, Amy Morton, makes a last-minute appeal to Booth, the man who arrested Epps, to re-examine the case. Booth believes Epps is guilty, but acknowledges that the case had a few loose ends. He asks Dr. Temperance Brennan and her team of squints to review the evidence and confirm Epps' guilt. But when Brennan finds forensic anomalies in the case, and Booth turns up evidence that another man was with April Wright the night she died, they must race against the clock to stay the execution.

Brennan's former forensic anthropology professor - and ex-lover - Dr. Michael Stires, surprises her with a visit to her lab at the Jeffersonian while in town to interview for a job. While they make plans to have dinner together that evening, Booth wheels in a soiled refrigerator, revealing the decomposed remains of a young woman inside. As Brennan and her team go to work to uncover clues as to what may have happened Booth discovers an old ransom note sent to the girl's parents shortly after she disappeared. Booth and Brennan determine the supposed kidnapping was a hoax and Booth makes an arrest in the case. When Bones is called in as an expert witness, she is shocked to discover the defense has brought in an expert of their own.

Construction workers find a skeleton in an old fallout shelter from the 1950s and the Jeffersonian is brought in to help identify the remains. When Zack cuts into the bone, he accidentally releases spores of the deadly fungus Valley Fever, causing the team to be quarantined in the lab over Christmas. While everyone tries to maintain the holiday spirit, Brennan buckles down to solve the mystery of the fallout shelter. Booth and Brennan's team are reminded that this is a rough time of year for Brennan, since her parents went missing right before Christmas when she was a kid. As Brennan works to bring closure to the family of the missing man - something she has yet to receive about her own parents - the time spent together in the lab provides the catalyst for revealing information about all of them.

Dr. Temperance Brennan and FBI Special Agent Seeley Booth travel to Los Angeles to determine the identity of a woman whose body parts were found near Los Angeles International Airport. With Booth at the wheel of their convertible rental car, they are assisted on the L.A. end of the case by young FBI Agent Tricia Finn, who is a little too eager to help. Agent Finn knows Brennan's books inside and out and mentions reading in an entertainment industry trade paper that the film rights to Brennan's latest book were bought by producer/director Penny Marshall. When Brennan and Marshall meet face to face on the set of "Entertainment Tonight," both Marshall and ET's Jann Carl are impressed and a little taken aback by Brennan's dedication to her latest case. Brennan's skills are put to the test when she realizes the victim's identity is hidden by previous extensive plastic surgery.

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. In two days he is scheduled to testify before a grand jury that his company has been sending defective body armor to Iraq. Decker suspects his former bosses may have had his wife killed and kidnapped his son in order to keep him quiet. When a shocking clue is sent to Booth as a warning, Brennan is able to use the clue to pinpoint the kidnapper's location and must race to save the boy's life.

Special Agent Seeley Booth enlists Dr. Temperance Brennan's help when a decomposed body is found in a local alley and the cause of death is unknown. As Brennan tries to assess if a murder has been committed, the details of the case draw her in deeper, and she's determined to help Booth find the teen's killer. As their investigation reveals the body is that of a teenage boy who had only comic books for friends, Brennan finds she may have more in common with the lone teenager than she though.

Booth and Brennan investigate when an El Salvadoran gang member is stopped with a dug-up corpse of a young woman in the trunk of his car. While he's being questioned, a drive-by shooting at the site gives the suspect a chance to escape. Booth and Brennan are able to find where the woman was buried - a soon-to-be-excavated community garden - but when they investigate her vacant grave, they find a second empty grave as well. Clues lead them to a wealthy senator's house where the gang member worked, and the investigation gets more complicated as nobody is willing to offer up the truth.

Brennan and Zack are called to the crash site of a small jet carrying Chinese diplomats and one mystery female passenger. At the scene, Brennan discovers three small bone fragments that didn't come from the plane and might have something to do with a local man who went missing five years earlier. After Dr. Goodman orders the squints to focus their efforts solely on the Chinese diplomat case, the missing man's son, Jesse Kane, shows up convinced the bone fragments are from his missing father. Brennan and the squints work to solve a mysterious murder involving a scheming younger woman and a local maintenance worker while keeping Goodman in the dark. As the forensic evidence mounts, Brennan must consider the possibility that Jesse had something to do with his father's death.

When Brennan is about to meet an online date for the first time at a local restaurant, she only barely escapes being the target of a shooting and she and Booth are trying to track down her attempted killer. Was it the man she met online? Or is it someone connected to one of the two bodies she's investigating - the victim of a mob hit and the victim of a serial killer? Brennan is not deterred and insists on continuing all the investigations, while Booth sticks close by her side - until he's the victim of a bomb explosion, rigged to Brennan's refrigerator. With Booth hospitalized, Brennan gets protection from Agent Kenton of the FBI, but FBI protection is not enough and Booth must race to save Brennan's life.

When the remains of a young documentary filmmaker are found in a ventilation shaft in an underground Washington, DC, tunnel, Brennan and Booth must venture into the maze of tunnels beneath the city and are surprised to discover a world of homeless shelters underground. Clues lead them to suspect that a man living underground was involved with the murder, but instead he gives them valuable information about the purpose of the victim's underground project. When a valuable artifact is found among the victim's possessions, the entire Jeffersonian team joins in the investigation to learn why the victim was in the maze of tunnels and what she found down there that led to her murder.

While on vacation in the desert, Angela contacts Brennan to ask for her help in identifying a skull - she's afraid it's her boyfriend, Kirk, who left on a photo shoot and has been missing for several days. The skull is sent to the lab, where Zack and Hodgins confirm that the victim died of a gunshot wound, had traces of peyote in his hair, and, sadly, is Kirk. Booth thinks the murder is drug-related, but the investigation leads them to a counterfeiting ring in the middle of the desert.

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. Hodgins is excited to get out of the lab and participates in a dive that uncovers more skeletal remains, which are authentic but prove that some of the bones found were actually stolen from the Jeffersonian collection. The investigation uncovers the possibility that the skeletal remains were placed at the dive site by a surprising culprit with a selfish motivation. But when the suspect is found murdered, a new lead sends the duo on the search for the owner of the dig shaft. Hodgins, excited to get involved in the case, volunteers for another dive in the shaft, but Brennan and Booth must race to save him from an underwater death when they discover who's behind it all.

When Brennan wakes up in the bathroom of her New Orleans motel room, bloodied, beaten up and her earring ripped out of her ear, she doesn't know what happened or how she got there, and discovers she's lost an entire day of her life. The circumstances and her loss of memory are enough to rattle even Brennan, who's in New Orleans on vacation, helping to identify victims of Hurricane Katrina. Upon learning of Brennan's situation, Booth arrives on the scene to help her decipher her lost day. When the local medical examiner in New Orleans is found murdered, Brennan is targeted as the prime suspect. Booth and Brennan's investigation leads them into the dark underworld of Southern voodoo, but their search for answers may not come in time to clear Brennan's name.

Booth's boss, FBI Deputy Director Sam Cullen, is anxiously awaiting information from doctors as to why his daughter Amy is dying of a rare form of lung cancer. When Brennan learns of Amy's condition, she questions the rarity of the cancer in a girl of Amy's age and background and discovers Amy had a bone graft as a result of a previous accident. Brennan enlists Booth's help to dig deeper into the origin of the bone graft she received, and they are shocked to learn Amy is not the only person with the rare terminal cancer and that she may be the victim of a crime.

Booth and Brennan investigate the apparent suicide of a protester in Arlington National Cemetery. But Brennan and her team discover this was not suicide, it was murder, and the victim was a soldier who had served in Iraq, not a war protester as originally thought. Booth and Brennan pursue the murder investigation and interrogate the American soldiers the victim served with in Iraq. Their investigation leads to many unanswered questions about the victim's military unit in Iraq and the actions they took while on patrol there. As they uncover more information about the case, all clues point to a potential military cover-up. Meanwhile, Booth laments the horrors of war and his own shady past as a military sniper.

While trying to determine the identity of a Jane Doe, Brennan is shocked to learn the remains are those of her mother, who went missing with her father 15 years ago. After years of uncertainty and not knowing what happened to her parents, Brennan finally has confirmation of her mother's death, and the news understandably hits her hard. Now that remains have been uncovered, Booth can open an investigation into the case for the first time. After researching Brennan's parents' lives, Booth surprises her with the news that her parents were not the people she thought they were - both were outlaws living under assumed identities. With the team working to glean more information from her mother's skeleton, to Brennan, she's now more of a Jane Doe than ever. As more details of her parents' past, in addition to her own, come to the surface, Brennan must come to grips with a whole new reality.