In this song, we are treated to a microcosm of mewithoutYou’s unique blend of Judaic, Christian, and Islamic imagery. Musically, we have the main driving guitar groove in the verses with a shimmery guitar over the top. We also have massive choruses featuring guest vocals by Jeremy Enigk of Sunny Day Real Estate and the clapping “fish is in the sea is in the fish” bridge.

First came a strong wind
Rippin’ off rooftops like bottlecaps
And bending lamp posts down to the ground
Then came a thunder, shattering my windows
But you were not that strong wind or that mighty sound
That left the barn in shambles
The rabbit hutch in ruins
The split-rail fence splintered and the curtains torn
All the cows out from the pastures
Trampling on the pumpkins
And the horses from their stables ambling in the corn

This is a reference to 1 Kings. After experiencing several phenomena (a wind, and then a fire), Elijah finally hears God whispering to him. So something came along and caused a lot of devastation, but God wasn’t the strong wind or the loud sound that destroyed everything. Though not mentioned specifically in the lyrics, the ego or the separate self would presumably be the cause of the devastation.

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Isa ruhu-lah ‘alaihis-salat was-salam
Isa ruhu-lah ‘alaihis-salat was-salam

“Jesus the Soul of God, peace and prayers be upon him”

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I’ve flown unnoticed just behind you like an insect
And I watched you like a falcon
From a distance as you passed
Then swooped down to be nearer
To the traces of the footsteps
To pick the fallen grain
From the pressed down dirt and crooked grass
And I’m gonna take that grain
And I’m gonna crush it all together
Into the flour of a bread
As small and simple and sincere
As when the dryness and the rain
Finally drink from one another
The gentle cup of mutual surrendered tears!
Come on!

This verse strikes me as a perspective change from Aaron to God. God follows him and is going to pick up the grain that fell down during the storm, make it into flour, and mix that flour with the bread, bringing together the grain that fell with the storm that caused it to fall in a sort of reconciliation. They would no longer be separate, but they would surrender to each other (drink from one another).
Alternatively: now Aaron is actively pursuing God.
Before looking at the lyrics, I had always taken it as “Finally drink from one another / The gentle cup of mutual surrender. Cheers! / Come on!” I suppose it still works, but it’s nice to know the real words.
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A fish swims in the sea
While the sea is in a certain sense
Contained within the fish!
Oh, what am I to think
What the writing
Of a thousand lifetimes
Could not explain
If all the forest trees were pens
And all the oceans – ink?

A metaphysical explanation of how we are all in God, but God is in everyone as well. What could he possibly think about what is impossible to explain? The last bit is a poetic interpretation of verse 31:27 of sūrat luqmān from the Qur’an:

And if whatever trees upon the earth were pens and the sea [was ink], replenished thereafter by seven [more] seas, the words of Allah would not be exhausted. Indeed, Allah is Exalted in Might and Wise.

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Isa ruhu-lah ‘alaihis-salat was-salam
Isa ruhu-lah ‘alaihis-salat was-salam
Isa ruhu-lah ‘alaihis-salat was-salam
Isa ruhu-lah ‘alaihis-salat was-salam
Salam, salam, salam, salam

“Jesus the Soul of God, peace and prayers be upon him”

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Nastagh-firuka ya Hokan
Ya Dhal-Jalah wal-Ikram
Isa ruhu-lah ‘alaihis-salat was-salam

“We ask for your forgiveness, Oh Judge
Oh Lord of Majesty and Generosity
Jesus Christ, the spirit of God, peace be unto you”

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Ya Halim, ya Qahhar
Ya Muntaqim, ya Ghaffar!
La Ilaha ilallahu, Allahu Akbar!

Al-Halim (the Forbearing), Al-Qahhar (the Subduer), Al-Muntaqim (the Avenger), and Al-Ghaffar (the Forgiving) are a few of the 99 names of Allah used in Islam.
Additionally, the phrase “Allahu Akbar” means “God is greater” or “God is greatest”. The lines offer praise to Allah.