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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 Indomitable literally rolls through the text to raise the question of man's freedom. Billy is stolen by that ship, from the Rights of Man. The ship that kills Vere is the Atheist. The political and religious implications of the ships' names are important to understanding the story's moral landscape and Melville's key question about how "free" mankind really is. Melville begins the book with a discussion of the political upheaval of the western world at the close of the eighteenth century, the time of the tale.
Democracy is a new experiment, born of a desire for free trade, hence the merchant ship Rights of Man. The Indomitable, a British navy ship, is appropriately Vere's ship, for like his vessel, he is also considered indomitable; but it is for Billy that the ship turns viciously indomitable when he hangs from it. Vere, however, does not survive the Indomitable either. He is appropriately killed by the Atheist; after all, a killing ship would hardly be called Christian. The "meaning" of Billy Budd has been argued through most of this century, and its masterwork status comes from a continual interest in searching the text for strands of thought and complexity. It can be read as a Biblical allegory or a historical novel about British naval history, for both play key roles in the book.
There is no doubt that Melville's last, and unpublished, work is a 2classic of American literature--despite the fact that none of the characters are American, and the story takes place in European waters. Billy is the classic hero, once described in the text as a golden Greek type. He is universal in his appeal and spans the history of western civilization.