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If there is any character who changes as result of his experiences, it is Vere. Once the moment of crisis comes, when Billy strikes Claggart, Vere breaks down to his more human self. He becomes "unstable," according to his officers, and is obviously fearful of a mutiny on board the Indomitable. Throughout the court proceedings, Vere struggles to reestablish his self-control and show no emotion, but it is difficult for him. He feels he must carry out strict military law, but he feels that there is irony in so doing. The captain genuinely believes that the truly guilty party is the evil Claggart, but the fact of the matter is that the innocent Billy has committed the murder.
In order to maintain military order and rule, Captain Vere must demand Billy's death as punishment for the crime. Vere fears mutiny if the situation is not handled in the proper military manner; the irony is that Vere has not handled things correctly. He has chosen to investigate Vere's charge of mutiny in the secrecy of his own cabin; as a result, the captain becomes the only witness to the crime. Then he refuses to wait and turn the matter of the murder over to the admiral. In order to protect peace and calm on his ship, Vere wants an immediate hearing and quick justice.
When Billy forgives his accuser and says, "God bless Captain Vere" right before his hanging, the good captain realizes the irony of the whole situation. Billy, the peacemaker, has assured that there is no mutinous plan against the captain. With the death of Billy, the possibility of mutiny is greatly increased.
When Vere is shot in the chest, possibly by his French counterpart, and murmurs Billy's name in his dying hour, it is obvious that the import of what he has done has not escaped Vere. He does not call Billy's name in fear or remorse. He is calmed by his appeal to Billy, as if the Handsome Sailor's peaceful nature has come to Vere in his final hour.
There has been much discussion of whether Melville might be condemning or lauding Captain Vere; it is one of those unanswered questions left to the reader's interpretation. What is known is that Vere is an authority figure -- well meaning and fallible. He wants to act correctly and struggles to do so. The doggedness he pursues and his relative distance from other human beings leads him to a certain type of decision that might ultimately be more destructive to himself than to anyone. Like Billy Budd, Captain Vere's human condition proves to be tragic.