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The major theme of the novel is Innocence vs. Evil, both of which are presented as elemental human qualities. By nature, Billy is purely innocent, not quite childlike, but lacking in knowledge of evil. Claggart is pure evil, not quite explainable except as a flawed element of human nature. The question raised in the story is whether true innocence can exist in the world or will it always be crushed by evil or driven to "evil" in the form of frustrated response, such as Billy striking Claggart. Melville, by allowing innocence to be tragically defeated in Billy Budd, makes it clear that evil still reigns in the world and innocence will always have to struggle against it.
The minor theme is clearly related to the main theme, for it shows that there is a rational compromise between the extremes of innocence, portrayed in Billy, and of evil, portrayed in Claggart. Captain Vere stands somewhere between the two extremes. He represents reason, book learning, and authority. He is human and humane; therefore, he has trouble contending with the extreme forces of good and evil represented by Billy and Claggart. Since he is a fair man, he convenes a court to try Billy. He is convinced that the shipboard court must act in compliance with martial law. Well- meaning and somewhat compassionate, Captain Vere knows that man-made rules and reason can not discern real justice. He believes Billy's execution is wrong, for he was an eye witness to the murder and knows the ironic set of circumstances of Claggart's death. As he is dying, he is still haunted by the injustice, as shown when re repeatedly states Billy Budd's name.
The mood of the book is very somber. Billy Budd, the main character, fights against evil in the book and looses. All of Melville's writing is highly emotional, and ultimately sympathetic to character or cause.