Musically, the song starts with rain and a keyboard before the vocals enter with one cymbal. The instrumentation then includes an acoustic guitar in either ear and an electric guitar in either ear. The electric guitars drop out for “to an anchor ever-dropped”, but come back in with accordion and chimes after that glorious drum fill starting at “napping.” After the vocals finish, we get a discordant transition into a groove with a great bass line and some EBow action on one of the guitars. Everything drops out one by one until it’s just bass and drums, then just drums.

“I do not exist,”
We faithfully insist
Sailing in our separate ships
And from each tiny caravel-
Tiring of trying, there’s a necessary dying
Like the horseshoe crab in its proper seasons sheds its shell
Such distance from our friends
Like a scratch across a lens
Made everything look wrong from anywhere we stood
Our paper blew away before we’d left the bay
So half-blind we wrote these songs on sheets of salty wood

He sees him and some of his friends as punching above their weight on the spiritual path. They’re claiming transcendent things like “I do not exist”, but for the “I” to not exist, you must not actually exist, you must become one with everything else. Meanwhile, they’re sailing in their separate ships and they’re so disconnected they can’t see anything right (like the speck/mote or log/beam in the eye Jesus talked about in Matthew 7:3). Meanwhile, they’re writing bad songs on the salty wood of their separate ships.

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Caught me making eyes at the other boatmen’s wives
And heard me laughing louder at the jokes told by their daughters
I’d set my course for land
But you well understand
It takes a steady hand to navigate adulterous waters
The propeller’s spinning blades held acquaintance with the waves
As there’s mistakes I’ve made no rowing could outrun
The cloth low on the mast like to say I’ve got no past
But I’m nonetheless the librarian and secretary’s son
With tarnish on my brass and mildew on my glass
I’d never want someone so crass as to want someone like me
But a few leagues off the shore, I bit a flashing lure
And I assure you, it was not what I expected it to be!
I still taste its kiss, that dull hook in my lip
Is a memory as useless as a rod without a reel
To an anchor ever-dropped, seasick-yet-still-docked
Captain spotted napping with his first mate at the wheel
Floating forgetfully along, with no need to be strong
We keep our confessions long and when we pray we keep it short
I drank a thimbleful of fire and I’m not ever coming back
Oh, my G-d!

He’s claiming to have attained something spiritually but he’s still caught up in the material world. Checking out other peoples’ wives and desiring female companionship generally. His boat’s propeller has stopped (“held acquaintance with the waves” – Shakespeare, referencing someone who died at sea) and that’s bad because he can’t outrun his own mistakes without it. He sees himself as bad (tarnished brass, mildewy glass), and though he wants female company, he wouldn’t want anyone who could want him. At some point in the past Aaron has stated he used his faith and the band to make out with women (“bit a flashing lure”) but is done with it (because it was not what he expected it to be, and is now a useless memory).

So now he’s stationary (“Seasick, Yet Still Docked” is a Morrissey song about being far from where you want, helpless to get there, but sick anyway) or just floating along, letting his mind run his life instead of being in charge himself (“captain spotted napping with his first mate at the wheel”). He’s not really trying to live right, just going through the motions of what you’re supposed to do (keeps his confessions long and his prayers short).

Then he “drank a thimbleful of fire”, experienced a tiny bit of the Holy Spirit, and he’s forever changed. 

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“I do not exist,” we faithfully insist
While watching sink the heavy ship of everything we knew
If ever you come near I’ll hold up high a mirror
Lord, I could never show you anything as beautiful as You

At the end of the song, we get an idea of what the ships are supposed to symbolize, which is the knowledge of holy things (as opposed to being), such as the remembrance of scriptures. The line states that they are heavy, and they’re sinking them and turning toward God. Last lines may be a paraphrase of Rumi:

“You have no idea how hard I’ve looked for a gift to bring You. Nothing seemed right. What’s the point of bringing gold to the gold mine, or water to the ocean. Everything I came up with was like taking spices to the Orient. It’s no good giving my heart and my soul because you already have these. So I’ve brought you a mirror. Look at yourself and remember me.”