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.

Skinner's Room is a short story by William Gibson originally composed for Visionary San Francisco, a 1990 museum exhibition exploring the future of San Francisco. It features the first appearance in Gibson's fiction of "the Bridge", which Gibson revisited as the setting of his acclaimed Bridge trilogy of novels. In the story, the Bridge is overrun by squatters, among them Skinner, who occupies a shack atop a bridgetower. An altered version of the story was published in Omni magazine and subsequently anthologized. "Skinner's Room" was nominated for the 1992 Locus Award for Best Short Story.

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.