The fourth mate and his crew hadn't returned in their whaleboat from the island when the mutiny began. Captain Jernegan had gone below and left his first mate, Leonard Apes, in charge. Sensing the danger that was brewing, the Captain got out his rifle, the only firearm he had, and put it on the bunk in the first mate's stateroom.
Jernegan then called his wife and children from their stateroom to join him and the second mate for supper in the main dining cabin. Tempers were flaring on deck and the first mate was being challenged by the angry crew. When the disturbance on deck was heard below, the second mate went to help break it up. The first mate's arm was pinned by Clark and the second mate was immediately struck on the head and he was lashed to the wheel.
The badly beaten second mate shouted to the Captain not to come out because the crew was wildly drunk. Thinking of both his ship and his family, Jernegan put his wife and children in their stateroom and waited with his rifle in the saloon. As he listened, it was clear that the mutineers were in control of his ship.
Martha's Vineyard Museum R. H. Dana