A protagonist is a main character in a work of literature. The protagonist of "By the Waters of Babylon" is named John. He is the son of his village priest. He is not only the protagonist but the hero of the story.
John's father allows him to go on a journey to Place of the Gods, which is also a Dead Place. It takes courage for John to make this journey, but knows he needs to do it.
While in the Place of the Gods, which we would recognize as New York City, John realizes that the beings who built this now dead city are not gods, but human beings who destroyed themselves. He also recognizes that if this great city was built by humans, then he and his fellow villagers can also regain the knowledge and level of civilization once possessed by these people. He brings that good news back to his father, who tells him they must move slowly and not frighten their people.
John is a hero, because through courage and wisdom, he gains knowledge that will help his culture advance.