Death & Loss
In some ways the poem elegizes Lowell's cousin, to whom it is dedicated. Death is inescapable and inexplicable, and the poem works as an attempt to give death some meaning. The only death that seems to have any meaning is the whale's, and only because the speaker beseeches the whale to martyr itself, to "Hide/Our steel, Jonas Messias, in Thy side."
Does that mean the other deaths in this poem—all the sailors'—are in vain? Maybe, but maybe not. Man does have dominion over all other forms of life; the whale dies at the hands of men. Perhaps Lowell is naming their deaths as the cost of that dominance.
Faith
Lowell's faith in Catholicism was likely shaken, if not broken, by the time he wrote this poem. This is apparent in his writing. The Quakers who praise the God that did not save them seem foolish, as do the people on pilgrimage, whom he likens to cows. His incorporation of Greek myths likens his biblical references to myths. None of these myths end well in this poem; he sinks Odysseus's ship and says Orpheus's magic lute would not succeed here. Generally, this poem lands on a tone of disillusionment.
The sea
The sea in this poem is literal, but it also stands in for the unexplainable, violent actions of God. The sea cannot die, and it is endless. Often to man the sea has represented endless possibility, travel, sustenance, and hope, but this poem focuses on the dark underbelly of those things.
