“By the Waters of Babylon” is set in a post-apocalyptic, post-technological world where people hunt for their food with bows and arrows and their priests scavenge the “Dead Places” for metal. John, the protagonist and first-person narrator, belongs to the tribe of the Hill People and is the son of a priest. The Hill People consider themselves culturally superior to the rival tribe of the Forest People, and live by dogmatic laws that, among other things, forbid them from traveling east, crossing the Ou-dis-son river, visiting the Place of the Gods (which was destroyed in “The Great Burning”), and saying the true name of the Place of the Gods.
John’s father and the other priests teach John reading, writing, healing, and “magic,” and John is fascinated by the stories about the gods. The story follows John on his initiation quest, a journey he undertakes in order to be recognized by his tribe as a man and a priest. John chooses the path of his journey based on visions and his reading of signs in the natural world. John’s desire for new knowledge leads him to break many of the laws of his tribe. He travels to the Place of the Gods, even though he is afraid that he will die there. Instead, he discovers that many of the stories about the Place of the Gods are inaccurate. The island is not filled with magical mists, the ground is not burning with eternal flames, nor is it populated by spirits and demons. Instead, John finds a vast Dead Place, a city of ruined towers. As he explores the city and learns more and more, John’s sense of fear diminishes.
John explores an abandoned apartment full of items that he believes are “magic” but which are recognizable to the reader as defunct modern appliances—a sink, a stove, and electric lights. John spends the night there and has a vision of the city as it was in the time of the gods. The city was once full of gods, lights, and “magic,” and John understands that the gods possessed incredible knowledge and power that they did not always use well. John sees that the city was destroyed by poisoned mist and “fire falling out of the sky” in a terrible war between gods, and understands that this war created the other Dead Places. The next morning John searches the apartment, hoping to find an explanation for the destruction of the city, and he finds the body of the dead god—who he soon realizes is not a god, but a man. John realizes that the gods were in fact humans from an earlier society, and he returns home, fearless and determined to share his new knowledge with his tribe.
Upon John’s return, his father recognizes him as a priest and a man. John tells his father that the gods were not gods, and asks him to kill him as punishment for breaking the laws of the tribe. John’s father refuses, explaining that the laws change from generation to generation, but advises John not to share his discovery with the people of the tribe, cautioning that it can be dangerous for a society to acquire knowledge too quickly, and theorizing that the society of the “gods” was destroyed because they did so. John agrees, but he and the other priests begin visiting the Dead Places to gather books (and thereby knowledge) as well as metal. In the story’s closing lines, John vows that when he becomes the head priest of the tribe, he will lead his people to the Place of the Gods—which he now refers to as “newyork”—and begin to rebuild the city.