At the end of the short story “By the Waters of Babylon,” John, the protagonist, decides that the gods were not actually gods. Instead, he decides that they were men.
For most of the story, John takes for granted that the beings who made the dead places were gods. We hear that he is going to go to the “Place of the Gods” even though it is forbidden. He talks about the “god-roads” that are now falling apart. When he is inside the ancient city, he talks about “the ruins of the high towers of the gods.”
However, as John stays in an apartment in the city overnight, he has a vision of what the city used to be like. He also finds and looks at “the dead god” who used to live in the apartment. As he looks at the dead (and apparently mummified) body, it comes to him that this was a man and not a god. John says that
then I knew he was a man—I knew then that they had been men, neither gods nor demons.
This is an important realization because John then comes to believe that his people need to regain the knowledge of these past people. He comes to believe that they will be able to “build again.”
Thus, we can see that John decides that the beings that he previously thought were gods were actually human beings.