We begin our journey aboard a warship facing violent waves in the night. The sailors discover a body clinging to their net, so they weigh it down and throw it back in the sea. As he watches the drowned sailor sink, the speaker is reminded of Ahab, captain of the Pequod in Moby Dick, whose body would also be somewhere on the bottom of the ocean. Later, guns are fired to commemorate the sailor's death, and the deaths of others lost at sea.
The speaker wanders the Quaker graveyard in Nantucket, contemplating the sailor's fate and the fate of the Quaker sailors who died whaling. He imagines the Pequod trying to return home and failing, just as the sailors did. Meanwhile, the sea birds seem to be mourning all these deaths, and he hears both their cries and the cries of the Quaker sailors, whom he imagines still thought God was on their side even as they drowned. Even though the whaling industry may be over, he imagines that humans still believe that God is on their side, even as they defy him and die aboard great warships.
Briefly, he visits a religious shrine in England, where everything is peaceful but where it is impossible to see or understand what God is thinking. When he returns, the graveyard is dark and spooky and the sea is facing another violent storm. He imagines the whale, whom Ahab stabbed, spilling its guts into the sea, and that those guts are like man's corruption, slowly destroying everything. But he also imagines God creating man from the sea slime, starting life the same place that the sailors lost their lives. In the end, he supposes it is God's will who lives or dies, and that His will is beyond human understanding.