PKD continues a number of themes found in Do Androids Dream.. and most of his other stories: Drugs as a consumer culture, forced colonization, and people with psychic powers.

The influence of mind altering substances is central to the idea of Three Stigmata, though the substances themselves are merely a side effect of desiring an escape from the dreary and increasingly pathetic lives lived first by the colonists, and the character assume, inevitably the inhabitants of Earth as well. Escapism is crucial to the novel, and some broad philosophical questions are asked: Can people live with a comfortable lie? Is a pathetic existence better than no existence at all? A number of solutions are offered to those desiring something more in their lives: Traditional religion, evolutionary leapfrogging, chemical substances, and even reading.

PKD's novels are fraught with painful moments of loneliness, reminiscent of a late night spent staring at the ceiling. However, Three Stigmata takes this ennui and introspection and dials it upward, allowing the reader to wallow in the misery and self-awareness of the lives on the scorched Earth. Characters are cowardly, self-absorbed messes, struggling to live squalid lives in the shell of civilization. Psychology is provided by talking suitcases and automatic cabs. Everyone is abusing something or someone, and every day is more retched than the last. Three Stigmata  is an unusually emotional piece from PKD, and I look forward to the ending.