The book has three separate but overlapping stories, with the repeated appearance of shared characters. The San Francisco/Oakland Bay Bridge, the overarching setting of the trilogy, functions as a shared location of their convergence and resolution.

In the post Tokyo/San Francisco earthquake world of the early 21st century, Colin Laney is referred to agents of the aging mega-rock star Rez of the musical group Lo/Rez for a job using his peculiar talent of sifting through vast amounts of mundane data to find "nodal points" of particular relevance. Rez has claimed to want to marry a synthetic personality named Rei Toei, the Idoru (Japanese Idol) of the title, which is apparently impossible and therefore questioned by his loyal staff, particularly by his head of security, Keith Blackwell. Blackwell believes that someone is manipulating Rez, and wants Laney to find out who. Simultaneously, the Seattle chapter of the Lo/Rez fan club is discussing exactly the same topic of the unbelievable marriage of human and AI construct. Fourteen-year-old Chia Pet McKenzie is chosen by the group to go to Tokyo and meet with the Tokyo chapter to find out what is really happening. On the flight she meets a woman named Maryalice, who dupes her into unwittingly carrying a contraband item through customs in Tokyo.

The first strand of the novel follows Hollis Henry, a former member of the early 1990s cult band The Curfew and a freelance journalist. She is hired by advertising mogul Hubertus Bigend to write a story for his nascent magazine Node (described as a European Wired) about the use of locative technology in the art world. Helped by curator Odile Richard she investigates Los Angeles artist Alberto Corrales, who recreates virtually the deaths of celebrities such as River Phoenix. Corrales leads her to Bobby Chombo, an expert in geospatial technologies who handles Corrales' technical requirements. Chombo's background is troubleshooting navigation systems for the United States military. He is reclusive and paranoid, refusing to sleep in the same GPS grid square on consecutive nights, and only consents to talk to Hollis due to his admiration for The Curfew.

The plot centers around Chevette Washington, a young bicycle messenger who lives in the ad hoc, off-the-grid community that has grown on the San Francisco-Oakland Bay Bridge in the aftermath of a devastating earthquake. Chevette, on a whim, steals a pair of dark-rimmed glasses from a man at a party because she is offended by his demeanor. Soon after, she realizes that the glasses have unlikely importance, as security company henchmen begin tracking and following her. Among the pursuers are Svobodov and Orlovsky, two Russian immigrants who reside in San Francisco and are employed as cops, as well as Loveless, a ruthless corporate hitman with gold incisors. The glasses contain plans by a powerful corporation to rebuild San Francisco entirely using nanotechnology, and for that reason, they are highly coveted and present a danger to the person who possesses them.