Having just spent two months in Guatemala where she was identifying victims of genocide, renowned forensic anthropologist Dr. Temperance Brennan returns to Washington, D.C., where she is immediately detained by an agent from Homeland Security for carrying a human skull in her bag. Upon the arrival of FBI Special Agent Seeley Booth, Brennan is released, which she finds odd and realizes that it was his ploy to get her to help him on an FBI case. She refuses to help until Booth promises her full participation in the case, which he reluctantly does.
At the crime scene, Brennan and Booth find human remains which were so thoroughly decomposed that only the bones remained. Brennan and her assistant, Zack Addy, determine the victim is a woman between 18 to 23 years old, and was a tennis player. Back at the Jeffersonian Institute, Brennan argues with her boss, Dr. Daniel Goodman, who feels no qualms about assigning her to work with other federal agencies without her permission.
Inside the Medico-Legal Lab of the Jeffersonian Institute, Brennan examines the victim's remains while her colleagues inquire about the resemblances between them and the characters in her new book, Bred in the Bone. Dr. Jack Hodgins, an entomologist, tells Brennan that the victim has been in the pond for more than two summers. Hodgins has also found small bone fragments in the silt, which he guesses are rana temporaria or simply, frog bones. Angela Montenegro, a forensic artist, uses a computer program she has developed, called the Angelator, to make a three dimensional holographic reconstruction of the skull, which Brennan reassembled. The identity of the victim is revealed to be Cleo Louise Eller, who was a missing senate intern and was rumored to have had an affair with Senator Alan Bethlehem.
Brennan wants to confront the Senator but Booth argues that the Senator is not the only suspect. The Senator's aide, Ken Thompson, was Cleo's boyfriend. There is also Cleo's stalker, Oliver Laurier. Booth tells Brennan that they have a major case and that FBI Deputy Director Cullen is going to want to set up a special unit to investigate, which means they are going to have do things by the book and wants her to stay at her lab. Brennan blackmails Booth until he agrees to let her come with him into the field.
Based on the particulates embedded in Cleo's skull, Hodgins determines that Cleo's skull may have been smashed by a sledgehammer on a cement floor and diatomaceous earth. By the distinctive damage done to her finger pads and the way the body was hidden, the team determines that the murderer had put a lot of effort into hiding the victim. Hodgins also reveals that Cleo was taking medicine for her depression, while Brennan realizes that the small bones found with Cleo's body are not frog bones but fetal ear bones, indicating Cleo Eller was pregnant.
Hodgins, a conspiracy theorist, convinces Brennan that they may never find the truth as Senator Bethlehem may have enough power to impede the investigation. Without telling Booth, Brennan decides to confront the Senator. Consequently, Deputy Director Cullen removes Booth from the case but Brennan refuses to give up. With the help of her fellow scientists, she uncovers that Cleo Eller's boyfriend Ken Thompson, had killed Cleo because he feared the scandal Cleo's pregnancy would cause and affect his career. Brennan confronts Ken as he's about to set the crime scene on fire and shoots him in the leg to stop him. Booth arrives and arrests Ken.
The team and Booth attend Cleo's funeral. Booth comforts Brennan, telling her that what she did brought closure to Cleo's family which is better than never knowing what happened to her. Brennan explains that her own parents disappeared when she was little and Booth tells her that he killed a lot of people as a sniper and wants to catch at least as many murderers to make up for it. Brennan jokes with him about a karmic balance sheet then offers him her help in doing so. The two walk off together.
- Main article: Pilot/Characters
- Temperance Brennan - Emily Deschanel
- Seeley Booth - David Boreanaz
- Jack Hodgins - T.J. Thyne
- Angela Montenegro - Michaela Conlin
- Zack Addy - Eric Millegan
- Daniel Goodman - Jonathan Adams
- Oliver Laurier - Chris Conner
- Sam Cullen - John M. Jackson
- Bennet Gibson - Dave Roberson
- Alan Bethlehem - Larry Poindexter
- Ken Thompson - Sam Trammell
- Ted Eller - Tyrees Allen
- Sharon Eller - Bonita Friedericy
- Peter St.James - Dominic Fumusa
- Cleo Louise Eller - Naja Hill
- Broken Bridge by Daughter Darling (Brennan falls asleep piecing together bone fragments to form the skull – US version.)
- Collide by Howie Day (Brennan falls asleep piecing together bone fragments to form the skull – international version.)
- Pain on Pain by Feeder (Brennan tells Angela that her most meaningful relationships are with dead people.)
- Gone by Thirteen Senses (Cleo's Funeral.)
- Dr. Temperance "Bones" Brennan, Special Agent Seeley Booth, Jack Hodgins, Angela Montenegro, Zack Addy and Daniel Goodman are all introduced for the first time.
- Bones makes reference to the next nearest anthropologist being in Montréal, Quebec. This is a reference to the character Temperance Brennan in the book series Bones, by Kathy Reichs, which the show is inspired by. Brennan in the novels is very different from the Brennan of the TV show. Brennan in the book is a forensic anthropologist from North Carolina who occasionally works in Montréal assisting with solving crime there. Brennan in this episode also asks Booth if he speaks French, in French. In both the book and the TV show, Brennan speaks conversational French fluently.
- The prop articles viewed by Booth weren't meant for high-definition display. They are clippings from The Washington Post from around the time of filming:
- The text from "Human Remains Found in Pond" is from "Making Globalization Work" by Sebastian Mallaby, Feb 28, 2005
- The text from "Body of An Unidentified Woman Found" is from "Martha Stewart To Leave Prison With New Image" by Frank Ahrens, Feb 28, 2005
- Booth refers to the characters of The X-Files in his remark, "We're Scully and Mulder", the investigating duo from the long-running television series.
- Booth refers to Zack as a "squint". "Squints" refers to how the lab assistants will solve a murder or look for a clue, even squinting their eyes sometimes to look.
- When Bones says a victim was of "mixed race," Angela asks, (while trying to reconstruct the facial image) "Lenny Kravitz or Vanessa Williams?" Lenny Kravitz shares Afro-American, Afro-Bahaimian, Russian-Jewish, and Eastern European ancestry.
- When Booth says, he needs to put all his ducks in a row before he can bring Bones out in the field with him.
- Brennan: "Angela, nothing Pete and I ever did was messy."
- Angela: "Then you weren't doing it right."
- Pilot summary from the archived official site of Bones
- "Bones" Pilot (2005) on The Internet Movie Database
- Bones: Pilot at TV.com
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