Who are the gods in ''By the Waters of Babylon"?
Stephen Vincent Benét's short story "By the Waters of Babylon" examines a post-apocalyptic world in which "the hill people," the presumed survivors of some sort of devastating disaster, lead their lives with distant respect for the gods. John, the story's protagonist and the son of a priest, embarks on a spiritual journey to the forbidden territory of the Place of the Gods. After a harrowing trip during which he is chased by dogs and must wander the land alone, John discovers a "dead god" in one of the buildings.
As it turns out, the "gods" in this story are actually the deceased victims (that is to say, ordinary humans) of the aforementioned disaster which destroyed civilization, and the Place of the Gods is the ruins of New York City. Although John has no context to fully understand these matters, his journey to this land makes him realize that it is necessary for the hill people to "build again."
In this story, the main character, John is going to go on a journey. It is the last step in his process of becoming a priest. On this journey, he will be going across the river to the Dead Place -- the Place of the Gods.
As we go along in the story, we figure out that the Place of the Gods is what used to be New York City. If that is the Place of the Gods, then the gods must be the people who used to live there. So, they gods in this story are the people who used to live in New York City before it somehow got depopulated.