The City and the Pillar narrates the journey of a man who remains captivated by the homoerotic desires stemming from his first schoolboy crush. Bernard Dick has highlighted how the novel elegantly extends the recurring motifs found in American literature, as seen in the works of Cooper, Melville, and Twain. These themes include the idyllic days of youth, the enigmatic allure of the sea, the pursuit of the unattainable, and the conquest of frontiers—here depicted as a cultural boundary. On a superficial level, the book presents a familiar narrative from the romance genre, focusing on a quest for something that ultimately proves illusory. The issue is not simply that Bob does not return Jim's affections when they reunite, nor is it that he hasn't embarked on a similar journey (despite Jim's belief that Bob, as his twin, must share his emotions). The truth is, Bob has genuinely forgotten their childhood idyll and its moment of forbidden erotic pleasure, as it held no special significance for him. This realization drives Jim to react with intense hostility towards Bob, with variations in each edition of the novel.

In The City and the Pillar, Vidal explores the inroads that experience makes upon innocence. The sexual relationship between Bob and Jim is portrayed as spontaneous and natural. As Jim’s sexual sophistication increases, sexual relationships become much more complex for him. As he realizes that the encounter with Bob was, for him at least, more than merely a casual release, he is forced to face his own homosexuality.

Vidal is saying essentially that homosexuality provides a reasonable but complicated sexual option and that one need not fit the stereotype of the homosexual in order to exercise that option. When Jim rushes out of the room to which he and his crewmate, Collins, have taken the two prostitutes, he hears Collins say, just as he is leaving, “Let the queer go; don’t mind him.” This remark festers, and when Bob, whom Jim has idealized for seven or eight years, calls him a queer, that catapults the drunken Jim into an action that results in his killing Bob. He is also killing the idealized vision that, in his own mind if not in actuality, led him into a homosexuality that he could neither accept nor overcome.