When Billy enters the captain's cabin and sees that Claggart is present, he is surprised, but not alarmed. He wonders if the captain plans to make Billy coxswain, thinking that perhaps Vere is going to ask the master-at-arms for a report on his performance.Ordering the sentry to admit no one, Vere directs Claggart to tell Billy face to face the story he had related to the captain, alleging Billy's part in a conspiracy. Claggart confronts Billy with a hypnotic stare and repeats his charge. Billy is speechless. When Vere orders him to speak in his own defense, Billy remains tongue-tied. Then Vere, sensing Billy's impediment, places his hand on the sailor's shoulder and quietly tells him to take his time.
Alter another instant's silence, Billy's right arm lashes out, striking Claggart on the forehead. The master-at-arms falls to the deck, dead. With a whispered exclamation of shock and compassion, Vere tries with Billy's help to revive Claggart, but it is "like handling a dead snake."
Soon regaining his official composure, Vere orders Billy to wait in a rear stateroom. He summons the ship's surgeon, who with one glance knows he is viewing a corpse, and then confirms Claggart's death with the usual tests. The captain emotionally exclaims that Claggart is an Ananias, "struck dead by an angel of God" who must hang for his deed.
The captain and the surgeon put Claggart's body in the stateroom opposite Billy. Vere informs the surgeon that he will quickly call a drumhead court and asks him to tell the ship's officers and Mr. Mordant, captain of the marines, but to request them to keep silent about what has happened.