The story, a recording of a medium's meditation over the future writing of the text, details the narrator, Adam Jeffson, on an expedition to the North Pole during the 20th century on board the Boreal. Jeffson's fiancée, the Countess Clodagh, poisons her own cousin to secure a place on the ship for Jeffson, because the expedition was known to be one of the best ever planned. A millionaire, who died some years previously, had provided in his will for the payment of millions of dollars to the first person to reach the Pole.
Before Jeffson leaves, he hears a priest speaking against polar research, calling the failure of all previous expeditions the will of God, and prophesying a terrible fate for those who attempt to go against God's will. Jeffson remembers meeting with a man who claimed that the universe is a place of strife between vague "powers", "The White" and "The Black", which vie for dominance.
Throughout the polar journey, Jeffson discovers that his course has been guided by these mysterious forces. He finds a huge lake of spinning water, with a rocky island inlaid with inscriptions. Upon seeing this, Jeffson faints. When he returns to his camp he feels nauseated after having smelled a peculiar peach-like odour. He also notices a moving purple cloud, spreading in the heavens. During the journey, he discovers dead animals, all without injury, and he learns of the death of his crew.
The ship being fairly easy to operate,[15] he sets out by himself. First, he travels towards northern islands, but upon seeing the death of all various races from around the Earth there (the result of an exodus, escaping the death-bringing cloud), and meeting ships crowded with corpses, he comes instead to the dead continent, walking through London, searching for news of the cloud. He looks for any survivors, but finds all barricades broken through by mad crowds. Later, he goes to the house of Arthur Machen (a close friend of Shiel's), whom he finds dead, having been writing a poem until the very end. There, he finds the notebook into which he writes his whole narrative.
The later parts of the book describe Jeffson's descent into mad pompousness: adopting Turkish attire, he declares himself monarch and burns down cities (including Paris, Bordeaux, London, and San Francisco) for pleasure. He then commits his life to one task, the construction of a huge and colossal golden palace on the isle of Imbros, which he means to dedicate as an altar to God and a palace to himself. He spends seventeen years on the palace, several times abandoning the work, until its completion, when he recognises the vanity of it.
While travelling through Constantinople, which he also burns down, he meets a twenty-year-old naked woman who is without the slightest knowledge of anything in the world. She continues to follow him, no matter how he mistreats her. Gradually, he accepts her, but forces her to wear a veil over her mouth. Her speed at learning astonishes him, so he teaches her to speak, read, cook, fish, and dress. The girl (who is unable to pronounce "r", instead saying "l") reveals that she had lived her whole life in a cellar below the royal palace of Turkey, and that she knew nothing of the world until she was freed when Jeffson burned down Constantinople. She becomes absorbed in the Bible and declares the humans who sought for riches as "spoiled".
Jeffson struggles mightily against his growing affection towards the girl, wishing to end the human race. At the end, when he leaves to go to England, she telephones him about the re-appearance of the Purple Cloud over France. He rushes to her, embracing her as his wife and now hoping to find a way to escape the cloud. She tells him to trust that God will not allow her to die. He concludes his writing by saying that he has accepted his role and that after three weeks have passed no purple cloud has appeared, and he looks forward to the two of them becoming the progenitors of future humanity.
