The show begins in the year 2005, and tells the story of a series of case files, solved weekly, by an unlikely alliance between Dr. Temperance "Bones" Brennan's forensic anthropology team at the Jeffersonian Institution (a thinly veiled allusion to the Smithsonian Institution) and FBI Special Agent Seeley Booth. By examining the human remains of the murder victims, Dr. Brennan and her team provide scientific expertise and an outsider's perspective to the world of criminal investigation to the FBI. In addition to the murder cases featured in each episode, the series explores the backgrounds and relationships of the major characters including the developing friendship and possibly romantic relationship between Brennan and Booth.

The concept of Bones was developed during the latter part of the pitching season of 2004 when 20th Century Fox approached series creator Hart Hanson with an idea of a forensics show. Hanson was asked to meet with executive producer Barry Josephson, who had purchased the rights to produce a documentary on the forensic anthropologist and author Kathy Reichs. Although Hanson was reluctant about being involved in making a police procedural, he signed on and wrote the pilot episode after having an intensive meeting with Josephson about the show. As the show is based on the works of Reichs, the writers constantly involve her in the process of producing the episodes' storylines.

In order to make Bones a unique crime drama in the midst of the multiple procedural dramas that already populated network television like the Law & Order and CSI franchises, Hanson decided to infuse the show with as much dark humor and character development as possible. Another element conceived for the show was the "Angelator", a holographic projector whose use is to replace flashbacks that are often used by other procedural shows. In addition to their expositional purposes, the holographic images, which are created by visual effects, brought a unique visual style to the show that the producers were looking for.

David Boreanaz was the first actor to be cast in Bones. Series creator Hart Hanson described the actors who had auditioned for the role of Seeley Booth as "pretty boy waifs" and immediately responded when the head of the studio, Dana Walden, suggested Boreanaz for the role. Boreanaz was offered the role but was unenthusiastic about getting involved after a difficult meeting with executive producers Barry Josephson and Hart Hanson, even though he thought the script was well written. However, after the producers contacted him again to convince him to accept the role, Boreanaz agreed to sign on and was cast as Seeley Booth.

Emily Deschanel auditioned for the role of Temperance Brennan close to the production start date of the series pilot, during which time another actress was nearly cast in the role. After the filming of Glory Road was completed, producer Jerry Bruckheimer told Deschanel about the role and sent her to Bones' executive producer Barry Josephson to audition for it. Deschanel impressed Hanson at her audition, where she showed the character's assertiveness by stepping forward towards Boreanaz after he moved towards her, to which Hanson remarked that "90% of actors would take a step back". She was subsequently cast in the role.

In Season 4, Zack Addy has been replaced by a succession of lab assistants. One -- Michael Badalucco, formerly of The Practice -- is much older than the typical grad student. On October 20, 2008, TV Guide reported that Marisa Coughlin will guest-star in a midseason episode as FBI agent Payton Perotta.

The title sequence of Bones is usually shown near the beginning of the episode. Accompanied by the show's theme music, composed and performed by The Crystal Method, the sequence provides the credits of the show. Each episode usually begins with a cold open, which sets up the plot of the episode and can last from three to ten minutes before the title sequence is shown. The title sequence varies from season to season. The first season's title sequence mostly consists of scenes from the first five episodes of the series while the second season's title sequence is made up of scenes from the first season and early episodes of the second. The opening credits in the title sequence include the regular cast members of the respective seasons.