"By the Waters of Babylon" has two settings. The entire story takes place in the future, after a nuclear holocaust has destroyed the advanced technological civilization of people like us.
The story's action begins, after some background, with John, the priest's son, outside of his village, fasting on a flat rock. He lives close to nature, apparently much like a Native American in centuries gone by. He takes an eight-day journey through the wilderness to arrive at what he calls the Place of the Gods.
The Place of the Gods is the other setting of the story. It becomes evident to the reader that this is what used to be New York City. John marvels at what he sees there: tall towers, a broken statue of George Washington, paintings, a cooking place but no wood, lamps but no wicks.
John realizes that the people who built the city were not gods, but humans. He goes back to his village determined to learn more about this lost civilization.