第 2 季 共 21 集
播出时间：2006年8月31日
第 1 集 The Titan on the Tracks
播出时间：2006年8月31日
A train carrying a popular Senator is derailed by a car positioned on the tracks. Brennan works out why the dead body of a rich businessman was placed in the car, and the search continues for her father. The team has a new boss.
第 2 集 Mother and Child in the Bay
播出时间：2006年9月7日
When the remains of a young pregnant woman and fetus are found in the Delaware Bay and identified as a newlywed who disappeared a year earlier, the investigation is aimed toward her husband, but takes a surprising turn. Booth is upset that his ex-girlfriend is letting their son spend time with her new boyfriend.
第 3 集 The Boy in the Shroud
播出时间：2006年9月14日
When the body of a young man, who's been missing for nearly three weeks, is discovered, the investigation leads them to his girlfriend, who is a foster child. Bones becomes emotionally involved in the case since, she too, became a foster child after her parents disappeared.
第 4 集 The Blonde in the Game
播出时间：2006年9月21日
After digging up the skeletal remains of a young girl, the investigation points to a convicted serial killer on death row. The team follows cryptic clues that lead to another body, an accomplice, and a victim who may still be alive.
第 5 集 The Truth in the Lye
播出时间：2006年9月28日
There are two suspects with the same motive when Booth and Brennan investigate the murder of a man found in a bathtub full of chemicals. They soon discover that he had two wives and a girlfriend.
第 6 集 The Girl in Suite 2103
播出时间：2006年10月5日
Booth and Brennan investigate a death due to an explosion in a Miami hotel. The clues lead to foreign diplomats with diplomatic immunity.
第 7 集 The Girl with the Curl
播出时间：2006年11月2日
The team investigates the death of a 10-year-old beauty pageant star. The other contestants, their parents, and their siblings all become possible suspects. Hodgins and Angela go on a date that actually goes well, despite what everyone else predicted.
第 8 集 The Woman in the Sand
播出时间：2006年11月9日
When the skeletal remains of a federal prosecutor who disappeared five years earlier are found in the desert outside Las Vegas, the team suspects it to be tied to the mob. Booth and Brennan go undercover as Vegas high-rollers in an attempt to uncover the mystery, Booth risks his life.
第 9 集 Aliens in a Spaceship
播出时间：2006年11月16日
The bodies of twin boys, kidnapped five years earlier, are discovered. The investigation lead Booth and Brennan to a notorious kidnapper known as the Grave Digger. During the investigation, Brennan and Hodgins become the Grave Digger's next victims.
第 10 集 The Headless Witch in the Woods
播出时间：2006年11月30日
While investigating the death of a film student who was working on a documentary about the legend of a headless witch, who haunted woods in the 1700's, Brennan develops a strong bond with the victim's brother.
第 11 集 Judas on a Pole
播出时间：2006年12月14日
Booth and Brennan are called to the scene where a man's body was found hung like a scarecrow, gutted, and burned on the roof of a building used by the FBI to hide witnesses.
第 12 集 The Man in the Cell
播出时间：2007年2月1日
The notorious serial killer, Howard Epps, sets his prison cell on fire as part of a daring prison escape. Brennan is his target and her entire team is placed in danger.
第 13 集 The Girl in the Gator
播出时间：2007年2月8日
Brennan has to work with another agent while Booth needs to see a therapist. The duo investigate the death of a college freshman, who took part in a 'Girls Gone Wild' type of video.
第 14 集 The Man in the Mansion
播出时间：2007年2月15日
Booth and Brennan investigate the death of Terence Bancroft, one of the Jeffersonian's major donors, found dead at his home. Hodgins' relationship with the wife of the deceased years earlier, compromises the case.
第 15 集 Bodies in the Book
播出时间：2007年3月15日
Brennan and Booth have to solve three murders that are identical to the murders in Brennan's new bestselling book.
第 16 集 The Boneless Bride in the River
播出时间：2007年3月22日
The team investigate the death of an Asian woman found without any bones left in her body.
第 17 集 The Priest in the Churchyard
播出时间：2007年3月29日
A broken water main uproots multiple coffins in an old graveyard. When the team is brought in to identify the bodies for re-interment, they discover a newer skeleton that should not be in the graveyard, which has not been used for 50 years.
第 18 集 The Killer in the Concrete
播出时间：2007年4月5日
Booth and Brennan investigate the case of a partial skeleton found in cement. Booth thinks a member of a crime family is responsible.
第 19 集 Spaceman in a Crater
播出时间：2007年5月3日
Brennan and Booth are called to the scene where a dead man has been found in a crater. The investigation leads them to the National Space Agency.
第 20 集 The Glowing Bones in the Old Stone House
播出时间：2007年5月10日
The team investigate a glowing body. Hodgins proposes to Angela -- several times.
第 21 集 Stargazer in a Puddle
播出时间：2007年5月17日
When Angela draws the face of an old woman to go with the decomposed skeleton of someone much younger, they soon learn the victim had Progeria, an aging disease. Booth and Brennan investigate to discover who would want to kill such a fragile person. Meanwhile, Hodgins and Angela's walk down the aisle doesn't go as planned.
