Based on the real-life experiences and best-selling works of novelist-forensic anthropologist Kathy Reichs, who solves crimes using evidence supplied by skeletal remains. The show follows Dr. Temperance Brennan, a bones specialist, doing her best to solve crimes for the FBI and Homeland security. In the pilot, Dr. Temperance 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 murderer turns out to be a politically sticky business. Special Agent Seely Booth, Bones' 'friend' bails her out of police custody, and she deduces the fact that it was a set up to get her to talk to him. Although nothing is said on the matter, it could be seen that the two may have had some relationship history, but this is just an assumption. Seely informs Bones of a peculiar set of bones found at the bottom of a lake in a graveyard. After viewing the bones (via an underwater camera), Bones declares that it is, in fact, a murder scene.
When the decaying corpse of the Venezuelan Ambassador's son is found hanging from a tree on the campus of an exclusive private school, a simple suicide case quickly turns into a web of lies, sex and scandal, involving the school's staff and students.
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, Zach accidently releases a deadly fungus, that causes the team to be quarantined over Christmas.
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.
FBI 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 thought.
Brennan and Booth investigate the site of a train wreck where the bodies of a senator and a high-profile businessman are found within the wreckage. The businessman's body is found in a car on the train tracks, and at first glance, it is an apparent suicide. While investigating a possible connection between the two victims, Brennan and her team discover the businessman is still alive, but severely injured, at a local hospital, and the body at the scene is someone else. As the clues begin to unravel, the investigation gets more complicated when details of the man's private life are revealed, leading Brennan and Booth to a private detective who may hold key information. Meanwhile, Brennan is introduced to Dr. Camille Saroyan, a first-rate pathologist who has been hired as the head of forensics at the Jeffersonian, and more importantly, Brennan's boss. It doesn't take long for Brennan to figure out "Cam" is a little too familiar with Booth and that they share something of a past. Also, Booth encourages Brennan to visit her mother's gravesite for the first time.
Booth and Brennan examine the remains of a woman and fetus found in the Delaware Bay. The body is identified as that of Carlie Richardson, a pregnant newlywed whose mysterious disappearance one year ago had been a major national news story. Carlie's husband Kyle Richardson is immediately thought to be the prime suspect in the case, but he disappears before Brennan and Booth can question him, prompting Booth to call for a manhunt for Kyle. Clues found with the remains throw suspicion in a different direction, and Brennan enlists Booth and her team at the Jeffersonian to recreate the potential scene of Carlie's murder to get a better idea of the build and body type of the murderer, with shocking results. Meanwhile, Booth is annoyed that his ex-girlfriend Rachel, the mother of his son Parker, is letting Parker spend so much time with her new boyfriend, forcing Booth to be more territorial than Rachel would like.
Brennan and Hodgins join Booth and Cam at a crime scene beside an overturned garbage truck. Among the trash in the truck is the body of a young man wrapped in a shroud. Brennan finds that his skull is cracked and his leg is broken, and Hodgins determines the victim has been in the trash heap for at least three weeks. At the lab, Angela is able to identify the body from a facial imprint created by the shroud. As Booth and Brennan try to unravel the limited clues of the case, the parents of the deceased boy point a suspicious finger at their sons young girlfriend, Kelly, a product of the foster system. Brennan takes her team members rush to judgment and criticism of Kelly to heart since shes a product of the foster system as well. When Kelly confesses to the murder of her boyfriend, Brennan and Booth dont buy it, but are shocked and disheartened to discover who the real murderer is. Meanwhile, things get tense when Brennan and Cam butt heads over their different work styles and Brennan recoils at Cams power plays. When a disagreement comes to a head, Cam threatens to start looking for Brennans replacement, even if it means losing the whole Jeffersonian team if theyre forced to take sides.
Moments after Booth and Brennan unearth the skeletal remains of a young girl, it becomes clear they aren't dealing with just any murder case. Hodgins, Zack and Cam confirm this back at the lab when they discover that the cause of death points straight to Howard Epps, a convicted serial killer who has been on death row for years; Brennan's previous testimony in his case gave Epps a stay of execution. Booth interrogates Epps, seemingly to no avail, but after finding a clue on the deceased girl that leads them to another young body - this one only a week old - they realize that Epps is forcing them to play a deadly game. As the body count rises, Brennan and her team scramble to decipher Epps' cryptic clues in a desperate effort to find his cold-blooded accomplice. The team is pushed even further when it is revealed that the latest victim may still be alive, with only hours left to live. As precious seconds tick away, Brennan and her team must test their limits and confront their fears to save a young girl from becoming a victim.