Lyric discussion by xypotion 

My theory is that it's a tragic love story that took place during World War II. The religious references are not the focus of the song, I think. It took me a long time to see it, but the context speaks of the bombing of Pearl Harbor.

First, Kingfisher was a bomber in the air force, or perhaps a fighter pilot. The stanza that illustrates that best is: "I can bear a lot but not that pall Kingfisher, cast your fly O lord, it happens without even tryin' When I sling a low look from my shuttering eye"

Other things like rations, "sounding the alarm" and "preparing for when the bombs hit" keyed me in to war at first, and there's more evidence later in the song that she's talking specifically about Pearl Harbor.

I think Joanna does switch narrators several times during the song. She sometimes sings as Kingfisher him/herself, but other parts are his/her lover addressing or observing Kingfisher. The "quiet" part at the end is more historic, and definitely speaks to me of the persecution of the Japanese after Pearl Harbor:

"We came by the boatload And were immobilised Worshiping volcanoes Charting the loping skies

The tides of the earth left Us bound and calcified and made as Obstinate as obsidian Unmoving, save our eyes"

The stanza: "I know you; you know me Where have we met before, tell me true? To whose authority Do you consign your soul?" Clinches the relationship between Kingfisher and the other character; S/he was a Japanese immigrant, and they were lovers before the war. S/he might have even been an actual Japanese spy, but that's not stated very clearly in the song. Now s/he is imprisoned on a military base (in Hawaii?), where Kingfisher sees him/her again.

"To whose authority / Do you consign your soul?" is a reference (almost a joke) about the Japanese' devotion to their emperor versus Americans' to the flag. What they did to the Japanese after Pearl Harbor was pretty atrocious.... The "dream" where Kingfisher kills the lover as if by an atom bomb (a basically undeniable Japan reference) is the final stroke. All hope is lost for the him/her, and s/he expresses his/her regret in the final stanza for the choices they each made.

They rest of the song, while beautiful and fully up to Newsom's poetic standards, says more about their love and less about what actually happened. It's still a love song, but with a historical context and a tragic outcome!

You're a genius! I would have never thought of WWII! The volcanoes work with Hawaii too.

Yeah! I'm usually terrible at figuring out songs, but this one clicked with me somehow. Joanna is the genius! :D

This is exactly what I drew from the lyrics too, a lot of Joanna's songs may have religious (not just Christian) aspects, but I really don't think she focusses on them that often... Usually there's some sort of deeper story there, about a person or people or it's coupled with religion for metaphorical purposes... She's no Sufjan Stevens, guys!

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