The idea of naturalism pervades Billy Budd. In the novel, it is closely linked with the narrator's inability to explain the behavior of two of his main characters: John Claggart and Billy Budd. The result of this inability is that there is quite a lot of philosophizing about what it means to be natural, to be connected with nature. Yet, unreliable as the narrator is, things begin to get confusing. With all of his speculation, it is unclear whether or not he is making the characters seem more natural or less, whether or not he really believes in naturalism or is simply hiding behind it because he can't explain his characters' motivations.
Whether or not Billy Budd's actions are natural, by idealizing them as such, the narrator actually makes them seem extremely unnatural and subject to close scrutiny.
As Captain Vere debates whether or not to execute Billy Budd, it becomes apparent that all of his learning has actually isolated him from his moral instinct. He is now capable of rationalizing over what he instinctively feels to be right.