Good versus Evil
Melville suggests there is an eternal conflict in the world between evil and good. Evil is represented by the master-at-arms, Claggart, and good is embodied in Billy Budd. Billy is repeatedly described as like Adam, the innocent first man, and is also presented as a Christ-figure. Claggart, on the other hand, is likened to Satan. It is his nature to do evil. He was born with that tendency already inside him. The malice he bears towards Billy cannot be ascribed to any rational cause, and Billy has given him no offense. But because Billy is innocent, he is defenseless against the wiles of evil. He cannot understand that it is simply the nature of evil to attempt to destroy good. In this case, the evil succeeds, and Billy dies. However, the principle of good is not as helpless as it first appears. Claggart also dies, since when Billy is provoked, he hits out with deadly force. This shows that when roused, good can combat evil with an equal force, although it cannot avoid eventually being destroyed.
The theme of justice centers around the character and actions of Captain Vere. On the surface it seems that Billy does not receive justice, since there are mitigating circumstances to his act. He was falsely accused by Claggart, and he did not intend to kill him. However, the military code of the day prescribed death as the penalty for striking an officer. Captain Vere is presented in a positive light as an intelligent, well-read, fair-minded man. He argues for the death penalty against Billy because he is concerned with upholding his duty, which is to maintain order and discipline on his ship. He believes this would be jeopardized by taking a lenient attitude to Billy.
The fact that Billy has to die suggests how hard it is for innocence to survive in the human world, and especially in a military situation. It is as well to remember that the incident on the Indomitable takes place during a war, and, as the novel makes plain, in the wake of two recent mutinies in the British fleet. Captain Vere upholds the strict letter of the law because the security of the nation is at stake, since the Navy is Britain's principle defense against its enemies. The point seems to be that in some circumstances, the individual, no matter how innocent, must be sacrificed for the welfare of the whole society. The position Captain Vere is placed in is not a comfortable one, and at a personal level, he sympathizes with Billy. But he places his duty above such personal feelings.