This one's pretty clear. Claggart is the bad guy. The narrator thinks that he is naturally depraved (corrupted; given to wrong actions) and suggests that he might be half-mad, that there is some elemental evil in him. For all that, it is still completely unclear why Claggart hates Billy so much. The narrator admits that he is leaving it a mystery because he just doesn't know. Part of the result is that Claggart is less than a human character. He gets painted as just bad but we have no idea why, no way to sympathize with him. This is not a shortcoming of the story. It's supposed to be a realistic aspect of it. Sometimes people just do things and we can't understand why. What is clear, though, is that Claggart despises Billy and falsely accuses him. Hence the antagonist.