These are the characters featured in the episode Pilot.
- Main article: Temperance Brennan
Temperance Brennan returns from a trip to Guatemala. It is mentioned that the reason she went to Guatemala because of a bad break-up with Pete. She is detained by the DHS after a confrontation with a DHS Agent. She is shown to be an incredibly hard worker, putting together a shattered skull overnight. She also is very smart, being able to understand many aspects of the victim without actually meeting her.
- Main article: Seeley Booth
FBI Special Agent Seeley Booth appears first after Bones gets held for questioning by the DHS. He agrees to take Bones with him to a crime scene at a lake where Bones had been found underwater. He doesn't believe that Bones' work solves crimes, that "real policework" is what solves murders.
- Main article: Angela Montenegro
Angela Montenegro is the first character to appear onscreen. She is a people person and can identify with both Bones, Hodgins and Zack as well as Booth. Her technology helps identify Cleo as the victim found in the lake and also the method by which she was murdered.
- Main article: Jack Hodgins
Jack Hodgins is known as the "Bug and Slime" guy. He also is a conspiracy theorist and makes claims that Booth wishes to cover-up the murder and makes claims about Monika Lewinsky, another intern famous for having an affair with a politician.
- Main article: Zack Addy
Zack Addy is Temperance Brennan's assistant. He is half-way through two Doctorates and is shown to be somewhat blunt and socially awkward. He is shown to be as gifted as Bones in his work, however is still looked down upon because he has not completed a single Doctorate.
- Main article: Daniel Goodman
Daniel Goodman is Temperance Brennan's superior at the Jeffersonian. She clashes with him over his role in her partnership with Seeley Booth.
- Main article: Oliver Laurier
Oliver Laurier is one of Bones and Booth's suspects, Cleo had taken out a restraining order against him and he claims to have loved her. Booth believes he killed Cleo because of his "unhinged" nature. He is at the Senator's house when the police search it and is at Ken Thompson's house when Bones shoots Ken for trying to burn the evidence that he murdered Cleo.
- Main article: Sam Cullen
FBI Deputy Director Sam Cullen appears when Booth appeals to him to get Bones out in the field, as per her request. He is the person Booth and Bones go to when they discover the victim's identity. After Bones attacks Ken Thompson, he gives Bones and Booth hours to close the case before a taskforce, headed by Special Agent Furst, takes over the investigation into Cleo's murder.
- Main article: Bennett Gibson
DHS Agent Bennett Gibson is the agent that follows Bones at the airport, and detains her for having a skull in her bag. Booth takes Bones from him when he arrives and picks her up.
Single Episode Characters
Senator Alan Bethlehem, played by Larry Poindexter, is the victim's boss. He was having an affair with her and was known to have had more with other interns. He is heavily implicated in Cleo's murder. Bones believes he killed Cleo, and clashes with Booth over her belief.
Ken Thompson, played by Sam Trammell, is one of the Senator's staffers and Cleo's boyfriend, he is present when Bones talks to the Senator and tries to stop her from collecting a chewing gum sample from a bin. He reappears when the police are searching the Senator's house. His tropical fish lead Bones to figure out that he is Cleo's killer. He murdered Cleo because he feared his job was in danger because of her pregnancy.
In "The Man on Death Row", Bones reveals Ken now had a life sentence in prison for killing Cleo
Ted Eller, played by Tyrees Allen, is the victim's father and is first shown being told by Booth and Bones that his daughter had been found dead. He also appears in a video that Booth watches of Cleo.
Sharon Eller, played by Bonita Friedericy, is the victim's mother and is first shown being told by Booth and Bones that her daughter had been found dead. She also appears in a video that Booth watches of Cleo.
Peter St. James
Peter St. James, played by Dominic Fumusa, is Bones' ex-boyfriend, he is first mentioned by Angela as the reason for Bones' trip to Guatemala. He later appears in Bones' house reclaiming his TV. Bones attacks him, fearing an intruder in her apartment. This character may be a reference to the book incarnation of Temperance Brennan's ex-husband.
Cleo Louise Eller
Cleo Louise Eller, played by Naja Hill, is the victim found at the bottom of the lake. She is known for having an affair with her boss, Senator Alan Bethlehem.