Initially, Billy is taken aback by the situation but does not feel afraid. Claggart advances towards Billy, staring him in the eyes, and repeats the accusation. It takes some time for Billy to comprehend what he is being accused of, and he becomes completely focused on it. Vere encourages him to speak up and defend himself, but the accusation terrifies Billy, causing his stutter to worsen. Despite trying to follow Vere's advice, Billy feels as though he is suffocating. He cannot speak and just makes noises.

Vere was unaware of Billy's speech impediment before, but he now realizes it, and understands it's a sign of nervousness and not guilt. He tries to comfort him, however, his words backfire as Billy becomes more anxious to impress. In his frustration, Billy's right arm suddenly strikes Claggart, causing him to fall to the ground, where he lies unmoving. Vere's demeanor shifts from being paternal to that of a strict military disciplinarian. He orders Billy to be confined in a stateroom and sends Albert to fetch the doctor.

The surgeon verifies the death of Claggart and feels uneasy upon seeing Vere, worrying about his emotional state. Vere commands the surgeon to inform the lieutenants and the marine captain of Claggart's demise and to instruct them to maintain secrecy about the matter. The surgeon is also directed to inform them that there will be a drumhead court.

Despite his concerns about the Captain's decision, the surgeon agrees to comply. He believes that it is unwise to do so and thinks it would be better to wait until they can reunite with the squadron and bring the matter to the attention of the admiral.