The central conflict in this text is the way that the individual is placed in conflict with the larger society of which he is a part. This is the theme that runs throughout this powerful text, and is apparent when Billy himself is taken from his own ship, called Rights-of-Man, and taken by Bellipotent, the war ship, in order to fight as part of the country's army. The meaning of this latter ship is "The God of War," and thus this section of the novel can be seen as symbolic of the way in which society strips individuals of their freedom and forces them to give up their liberties in order to serve society at large.
This is something that is highlighted in Captain Vere's decision to punish Billy by the letter of the law rather than go with his individual conscience and feeling that Billy is actually a good and innocent man. Captain Vere is thus a powerful example of the way that society forces men to ignore their own individual intuition and morals in order to pursue punishment according to society's dictates. Note how Vere is described in the following quote:
The father in him, manifested towards Billy thus far in the scene, was replaced by the military disciplinarian.
What Vere's natural state is, the "father in him," is replaced when Billy breaks society's law. That is, Vere is forced to act in a way that is, to him, unnatural, because of society and the way that it dictates behaviour. Again, the conflict of the individual vs. society is presented.