Geologist Andy Shaw is a professor at the University of Miskatonic in Arkham and his intention is to stop a high-profile and highly publicized scientific visit to Antarctica.
He explains that when he himself led the last expedition to Antarctica, he discovered ancient ruins and many dangerous secrets hidden behind a mountain bigger than the Himalayan mountains.
A small advance group, led by Professor Lake, discovers the remains of fourteen prehistoric life-forms previously unknown to science, and also unknown as plants or animals. Six specimens have been badly damaged, while the other eight have been preserved in pristine condition. The strata of the samples place them too early on the geologic time scale for the characteristics of the samples to have evolved. Some fossils from the Cambrian era show signs of the use of tools to carve out samples of food.
When the main expedition loses contact with Lake's party, Andy and his colleagues investigate. Lake's camp is devastated, with most of the men and dogs killed, while a man named Gedney and one of the dogs are absent. Near the expedition's campsite, they find six star-shaped mounds of ice with a specimen under each. They also discover that the better-preserved life-forms have disappeared, and that some sort of dissection experiment has been performed on both the unnamed man and the dog. Gedney, the missing man, is suspected of going completely insane and killing and mutilating everyone else.
Andy and a graduate student named Danforth fly an airplane across the mountains, which they recognize to be the outer walls of a vast, abandoned stone city, distinct from any human architecture. The creators of this lost civilization are called "Elder Things", for their resemblance to the creatures of myth mentioned in the Necronomicon. By exploring these magnificent structures, the men learn through hieroglyphic murals that the Elder Things first came to Earth shortly after the Moon was formed, and built their cities with the help of "Shoggoths"—people capable of performing any task. Biological entities created to take any form, and reflect any thought. There is an indication that all earthly life evolved from cellular material left over from the creation of the Shoggoth.
As more buildings are discovered, the explorers learn of the Elder Things' conflict with both the star-spawn of Cthulhu and Mi-Go, who arrive on Earth shortly after. The images also show the decline of their civilization once the Shoggoths gain freedom. As more resources are used in maintaining order, the etchings become disorganized and primitive. The murals also allude to an unnamed evil lurking within an even greater mountain range located outside the city. This mountain range arose in one night and certain incidents and events prevented the Elder Things from discovering it. When Antarctica became uninhabitable, even for the Elder Things, they soon moved to a large, underground ocean.
Andy and Danforth eventually realize that the missing giants from the advance party's camp have somehow come back to life and, after killing the explorers, return to their town. Andy and Danforth also discover traces of an earlier exploration of the Elder Things, as well as a sled containing the bodies of both Gedney and his missing dog. They are eventually drawn to the entrance of a tunnel, into the subterranean area depicted in the mural. Here, they find evidence of various Elder Things killed in a brutal struggle and the leisurely wanderings of blind six-foot-tall penguins, apparently used as livestock. They are then confronted by a black, bubbling mass, which they identify as a Shoggoth, and flee. On the plane, above the plateau, Danforth looks back and sees something that causes him to go temporarily insane, implying that he is the unnamed evil himself.
Andy concludes that the Elder Things are survivors of a bygone era who merely slaughtered Lake's group in self-defense or scientific curiosity. Their civilization is eventually destroyed by the Shoggoths, who now hunt giant penguins. He warns planners of the next proposed Antarctic expedition to stay away from the site.
