Like many of Dick’s novels, The Three Stigmata of Palmer Eldritch utilizes an array of science fiction concepts and features several layers of reality and unreality. It is one of Dick’s first works to explore religious themes.
Life for most colonists is physically daunting and psychologically monotonous so the UN must draft individuals to colonize. Most colonists entertain themselves using Barbie-like “Perky Pat” dolls and the multitude of accessories manufactured by Earth-based P.P. Layouts. The company also secretly creates Can-D, an illegal but widely available hallucinogen that allows the user to "translate" into Perky Pat (if the user is female) or her boyfriend Walt (if male). This allows colonists to experience an idealized version of life on Earth in a collective unconscious hallucination. P.P. Layouts employs several precogs to determine if possible new Perky Pat accessories will be popular.
Life on Earth is also harsh as the global temperature has risen to a level where one can no longer be outdoors without a personal air conditioning unit and Antarctica is the only suitable vacation spot.
Wealthy people often undergo “evolution therapy,” performed in the clinics of Dr. Willy Denkmal (German for Monument). This allows them to skip several stages of human evolution. Their craniums become large and bubble-like and the therapy may increase their intelligence, although the narrative insinuates that the extra brainpower is superficial. Devolution is also possible and occurs in some cases.
Emily's second husband tries to sell her pots to P.P. Layouts as possible Perky Pat accessories but Barney recognizes them as Emily's and rejects them out of bitterness.
Meanwhile, the UN rescues Palmer Eldritch’s ship from a crash on Pluto. Leo Bulero, head of P.P. Layouts and an "evolved" human, hears rumors that Eldritch discovered an alien hallucinogen in the Prox system and plans to market it as "Chew-Z," with U.N. approval, on off-world colonies. This would effectively destroy P.P. Layouts. Bulero tries to contact Eldritch but he is quarantined at a U.N. hospital. Both Mayerson and Fugate have precognitions of Bulero murdering Eldritch.
Meanwhile, Emily and her second husband sell her pots to Eldritch and undergo evolution therapy. This causes Emily to devolve and unknowingly recreate pots she previously concocted.
Under the guise of a reporter, Bulero travels to the artificial satellite of Earth where Eldritch holds a press conference. Bulero is kidnapped and forced to take Chew-Z intravenously. He enters a psychic netherworld over which both he and Eldritch seemingly have some control. After wrangling about business with Eldritch, Bulero comes to a seeming future Earth. Evolved humans identify him as a ghost and show him a monument to himself where he is to have killed Eldritch, an "enemy of the Sol System."
Bulero returns to Earth and fires Mayerson because Mayerson was afraid to travel to the satellite to rescue him. Mayerson accepts his conscription to Mars but Bulero recruits him as a double agent. Mayerson is to inject himself with a virus after taking Chew-Z, which will deceive the UN into thinking Chew-Z is harmful and cause them to ban it.
On Mars, Mayerson buys some Chew-Z from Eldritch, who appears in holographic form beamed down from a starship. Mayerson tries to hallucinate a world where he is still with Emily but finds that he does not control his "hallucination." Like Bulero, he finds himself in the future. Mayerson arrives in New York two years hence where he speaks with Bulero, Fugate and his own future self about the death of Palmer Eldritch. He also encounters several manifestations of Eldritch, identifiable by their robotic right hand, artificial eyes and steel teeth.
Eldritch offers to help Mayerson “become” whatever he wants. When a despairing Mayerson chooses death, he becomes one with Eldritch and Eldritch plans to allow him to die when Bulero kills Eldritch. Eldritch, meanwhile, intends to live on in Mayerson's form and enjoy the simple if arduous life of a Martian colonist.
Mayerson, stuck in Eldritch's body and mistaken for him, is indeed nearly killed by Bulero in the near future, but before the fatal shot can be fired he is awakened from his Chew-Z trance in the present—by Bulero, who has just arrived on Mars.
Bulero is willing to take Mayerson back to Earth but refuses to after learning that Mayerson did not inject himself with the virus as instructed. Mayerson is now confident that Bulero will kill Eldritch and stop him that way, so the sacrifice of taking the virus in order to ruin Eldritch's business is unnecessary; but he doesn't try to convince Bulero of this. Later, Mayerson discusses his experience with a Neo-Christian colonist and they conclude that either Eldritch became a god in the Prox system or some god-like being has taken his place. Mayerson is convinced some aspect of Eldritch is still inside him, and that as long he refuses to take Chew-Z again, it is Eldritch who will actually be killed by Bulero in the near future; Mayerson is half-resigned, half-hopeful about taking on the life of a Martian colonist without reprieve—after all, the Eldritch creature, with all its Godlike powers and history, seemed to covet that simple life. Mayerson considers the possibility of Eldritch being what humans have always thought of as God, but inimical, or perhaps merely an inferior aspect of a bigger and better sort of God.
Although he and the other Chew-Z users are still "unclean," occasionally tainted with Eldritch stigmata, everything Mayerson has heard and learned from his and Bulero's future experiences suggests that once Bulero kills Eldritch bodily, the Eldritch creature's influence and semblance will slowly fade from the universe, though it will take a long time; by choosing a boring but real life over Chew-Z, Mayerson will help bring this about. As unconventional as the story has been, here it actually approaches closure on the space opera level: the "good guys" who care about what happens to humankind will win, the Eldritch creature ultimately fail.
The final scene does not contradict this happy ending, but does black-humorously suggest some doubt. Bulero is returning to Earth, having realized that although the virus plot has failed, he still has a chance of assassinating Eldritch, just as Mayerson has foreseen. But meanwhile he and everyone around him has suddenly developed artificial right hands, Jensen visors, and steel teeth. This is not inconsistent with Mayerson's scenario—Eldritch is not yet dead, so the universe is still tainted—but reminds us that Mayerson may be wrong about how it will turn out, that there's also a chance Eldritch will triumph. For one thing, in the last instance of one of the book's running gags, the allegedly extra-evolved Bulero frequently seems more stupid than smart, and the fate of humanity now depends on his addled consciousness. In addition, it is mentioned earlier in the book that one of the Eldritch creature's favourite tricks is to meet people disembarking at airports and spaceports, to demonstrate precisely how inescapable it is; the novel finishes before the space flight lands, and so we never know whether Eldritch appears at the spaceport to mock Bulero.
All who try Chew-Z seem to have visions of Eldritch who appears to have control over their "afterlife." The title of the novel refers to Eldritch’s "three stigmata," his robotic right hand, artificial eyes (made, according the book itself, by "Brazilian oculists") and steel teeth. Eldritch does not develop a typical stigmata; the mysterious development of wounds similar to those of Christ during the crucifixion. Instead others develop a robotic right hand, artificial eyes and steel teeth: the "three stigmata of Palmer Eldritch."
Eldritch may be a Satanic figure in that he appears to be conniving and power-hungry, states himself to be a competitor to God (God promises eternal life. We can deliver it) and utilizes holy and otherworldly appearances for dubious ends. Mayerson theorizes that Eldritch is some aspect of God. In some theological views, Satan is one aspect of God or a necessary part of his court.
Eldritch may also be a Gnostic figure, reminiscent of the corrupting "blind god" Samael. Like Samael, Eldritch takes the existing world and changes it into his vision, thereby introducing "error," including suffering, unreality and entropy. Dick explored this perception of reality, the creation of a corrupting deity, in VALIS, The Divine Invasion and other works. Eldritch's three stigmata might bear a resemblance to the three aspects of the corrupting divinity of gnosticism. However, in many Gnostic tellings, the world is perfect before the arrival of Samael. The world of The Three Stigmata of Palmer Eldritch is not perfect before the arrival of Eldritch (it is indeed a stark and unwelcoming setting), and the Chew-Z dream world is less entropic than the real world (God promises eternal life. We can deliver it). It is possible that Eldritch is a reverse Samael, bringing the world out of a corrupted, entropic existence into an eternal one, but this too is a double-edged sword as Eldritch takes complete control of the dream world.
The novel also makes reference to Eucharist. Mayerson theorizes that it is perhaps not proper for the lesser being to consume the greater being and that the greater being should consume the lesser; i.e. the way Eldritch "takes over" those who take Chew-Z and the novel’s final scene, in which all people possess his "stigmata." However, the taking of Chew-Z could not be an inversion of the Eucharist if Chew-Z is Eldritch; the lesser beings are "consuming" him. But this could be another of Eldritch’s devilish tricks.
Among the Martian colonists, a man and a woman embark on a clandestine affair, which they will consummate as Perky Pat and Walt, using the drug Can-D. However, the other colonists soon take the drug and begin to share the experience. Disgusted, the lovers recover from their trances, and decide to do in reality what they could not do in unreality, before the others wake up.
In 2006, the book was adapted to a stage play by Polish director Jan Klata.