Sometimes, the Indomitable ship is separated from the rest of the squadron and assigned to special tasks because of the high regard for Captain Vere. Captain Vere is recognized for his capability to adjust effectively to unfamiliar situations, make prompt decisions when needed, and assume control during challenging circumstances.

On a particular expedition, the crew spots an opposing ship, which is revealed to be a military vessel. Despite being pursued by the Indomitable, the enemy ship manages to evade capture and escape. While returning to the fleet, the master-at-arms approaches Captain Vere, standing respectfully with his hat in hand, waiting for Vere's acknowledgement. However, Vere harbors an unexplainable aversion towards him. As soon as he recognizes the master-at-arms, Vere's face shows a unique and strange expression.

Claggart informs Captain Vere that while they were pursuing their target, he became convinced that one of the sailors posed a threat and that there was some secretive activity happening, which seemed to be instigated by the particular sailor in question.

Captain Vere is not excessively worried about Claggart's accusation, but he doesn't trust Claggart. When Claggart accuses "William Budd" of being a dangerous man, Vere is surprised. Vere cautions Claggart against committing perjury, but Claggart insists that his accusation is true.

Vere would rather not deal with the negative consequences of a thorough investigation, so he chooses to have Claggart confront Billy while he's there to observe. Vere instructs Albert, his hammock-boy, to fetch Billy and bring him to him.