The story is set in (then future) June 1994.
Bob Arctor is a member of a family whose members stopped using drugs. He leads a parallel life as Agent Fred who is an undercover police agent appointed to keep watch on Arctor's family members.
Fred / Arctor hides his identity from the people in drug subculture and from police. Though he starts off as pretending to be a drug user, he becomes addicted to the substance D(also known as slowdeath D). It is a psychoactive drug having a powerful effect on brain. This drug is derived from a small blue flowering plant called Clerodendrum ugandense.
In the process of finding the high level dealers of this substance D, he falls in love with a local drug dealer, Donna. His occasional use of drugs causes the two parts of his brain to function independently. This conflict results in strange situation in which Fred and Arctor don't realize that they are a same person. This situation leads to interesting and confusing chase.
Unable to understand this conflict, Fred starts to spy on Arctor. Upon a psychological test, Arctor's superiors at work find out that because of his drug addiction, he is unable to perform the task assigned to him effectively. Eventually, Donna takes Arctor to a rehabilitation center and it is revealed that Donna herself is a narcotics agent working for police.
Arctor is renamed "Bruce" in rehab center and he is forced to take part in group dynamics which break the will of the patients.
The story ends with Bruce working in a farming commune, suffering from a serious neurocognitive deficit after withdrawing from Substance D. Though he is considered just a walking shell by his handlers, he manages to spot blue flowered plant growing among corn . He realizes that these blue flowers are the source of substance D. He plucks these flowers and hides them in his shoes to give those flowers to his friends.
Reading this book is a very disturbing experience as the incidents in the novel make the reader feel very disturbed. The main reason for this is the ultimate life of Arctor who was an undercover cop at the beginning. The excessive usage of the term substance D too makes the reader feel disturbed.
