At the heart of Billy Budd are two characters that are twinned mysteries. To the narrator, one seems to be fundamentally good, the other to be fundamentally evil. Yet they are strange to him. He cannot understand why they are the way that they are. There are many other levels of foreignness in the book, and it is fascinating to see how the narrator's prejudices affect the way that he depicts events. Yet in Billy Budd what is so discomfiting is that even the most familiar seems strange. As much as the narrator focuses his energy on understanding Billy, Billy remains fundamentally "other" – a mystery.
The narrator of the novel has an inferiority complex that can be seen in his descriptions of Billy Budd and Captain Vere. He wants to consider himself of the same caliber as the two men, but he can't decide what distinguishes them from him.
As Captain Vere tries to determine what to do with Billy Budd, he loses his sense of his own identity. Overwhelmed by Billy's refusal to show signs of suffering, Vere himself takes on what he imagines Billy's suffering should be.