The Uncertain Nature of Reality
A fundamental issue of this novel, as well as an overarching theme of Philip K Dick's novels, is the question of reality: what is it, precisely? How do we know what we're experiencing is reality? This question is especially relevant to A Scanner Darkly: the main character, Bob Arctor, undergoes a psychotic breakdown as a result of an addiction to Substance D, and it is uncertain even to the reader what is really happening at certain points in the novel. By the story's end, Arctor's brain has been completely split in two, resulting in two separate personalities, Bob and Fred, who both see only half of reality. Appearances are deceptive in this novel as well; Donna turns out to be an undercover agent as well, and New Path, the rehab center, is actually a distributor for Substance D. All of these examples contribute to the novel's overall theme of the uncertainty of reality.
Substance Abuse
This novel is primarily about the substance abuse of Bob Arctor; the plot about undercover narcotics is less important than Arctor's character development. As Philip K Dick was a drug addict in real life, this explanation makes sense; this is his warning to his readers about the darkness of drug culture and the terrible effects it can have on one's brain. Accordingly, most of the novel's characters are either drug addicts or drug dealers, including Arctor, Freck, Fabin, Barris, Donna, and Connie. This substance abuse is at the heart of the novel, and Substance D is clearly an ambiguous stand-in for any number of real-world drugs that have a similar detrimental effect.
Paranoia
The characters in A Scanner Darkly are profoundly paranoid. It might even be justifiable to argue that the entire book is paranoid, characterized by extreme suspicion and mistrust even of itself. None of the characters fully trust each other, never quite sure if what they're seeing is real, a visual illusion caused by hallucinogens, a deliberate trick on the part of another person, or some other sort of deception. Everyone holds information back from each other, especially among the drug commune and Donna - both Bob and Donna are undercover narcotics operatives, Barris is synthesizing his own product and trying to frame Arctor, and everyone thinks Jerry Fabin is insane. The novel, moreover, proves these suspicions correct: even New Path, the drug rehab center, is the primary creator and supplier of Substance D. Paranoia seems to be justified in this novel, PKD's hint at the sort of terrible life led by those addicted to substances.
