Captain Vere had the task of informing Billy of his sentence. He went to the room where Billy was being held and the narrator admits he does not know what Captain Vere told Billy. He says it would have been in accordance with Vere's nature to tell Billy the role he (Vere) played in Billy's conviction. When Captain Vere left the room, he looked greatly pained, and the narrator thinks that he suffered even more than Billy from the result of the trial.
The narrator admits the limits of his knowledge, but guesses what might have happened between Captain Vere and Billy based on their natures and what he can interpret from facial expressions afterward. The narrator uses these clues to construct the narrative. Would someone else, witnessing the same things, have interpreted and told the story differently?