Both stories focus on a single young male character who is on a quest. In "By the Waters of Babylon," John is on a quest for the Place of the Gods because he has dreamed of it and wants to gain knowledge there. In "One Thousand Dollars," Gillian has inherited one thousand dollars and is on quest to understand how to spend it: he seeks knowledge by asking a variety of people what he should do with the inheritance.
Both protagonists meet with surprises on their quest. When he arrives at the Place of the Gods, which is, in fact, the ruins of New York City, John discovers that the people who lived there were not gods, but men. This gives John hope that his people can rise to rebuild their civilization to the level of the technological society that was destroyed.
Gillian likewise meets with a surprise when he spends the thousand dollars and learns that, depending on how he spent it, he will inherit another $50,000.
Both John and Gillian decide at the end it is better to keep some secrets. John doesn't reveal to his people that the beings they think are gods are men, and Gillian doesn't reveal to his lawyers the compassionate and generous way he spent his thousand dollars.