The story concerns an American naval officer who encounters a murderous and mysterious force and actions during an investigation in a balloon accident in the Swiss Alps.

Doctors declare that he has no chance of survival, but a nurse named Susan convinces them to operate on him and encourages him to keep his fighting spirit.

He deduces that this is an international effort since they died in different countries, and he also concludes that the final step of the operation would be his own death to eliminate all knowledge about the alien ship.

Monte Banks is revealed to be part of the Doomsday conspiracy, as he owns many industries that would lose money if they were not able to pollute.

Dan Brown, the author of The Da Vinci Code, named The Doomsday Conspiracy as the book that inspired him to write thriller fiction, citing its "simplicity of the prose and efficiency of the storyline".