The story of Through and Through, isn't clear to me. I've heard Kurt explain it as a story about losing one's religion, and I suppose that can be seen in the lyrics. Who better to describe it than the writer I suppose, but let's deconstruct anyway, shall we?

The first stanza:

Through a life of growing older
Gathering motes within a whirlpool
Displacing droplets from whatever lives above

"From whatever lies above".. is he describing the evolution of mankind here, and our dreamy nature to ascribe what we do not understand to what is beyond the sky? Possibly.

The next stanza:

Warm and protected in a cloud
And through it all
Reclining in my corner of a liar's amorphous plan

These lines seem to indicate a sort of opiate is at work here, on the unsuspecting public. Could it be religion? It has been described as an opiate in the past. An opiate would make a person feel good, like they are protected.

Next:

Tagging behind the millions
It held me so softly
I couldn't escape without vanishing

Sometimes, when we want to leave a religion, or better still, a denomination or cult, we have to do so by severing all ties to that religion, denomination or cult. We die to the people who are still inside, we vanish. These lines would suggest this sort of imagery it would seem to me.

And:

Looking up into the perforated ether
I saw myself swaying like a leaf
I followed beneath and cradled.
A deluge of the rest of everything
A universe and maybe more
With one leap I had shot ahead

A famous scientist once said something about education, specifically education in the sciences, causing religious students to either question their god, or at least force that god to be even bigger than they had at once believed. It was then that they realized that these students no longer believed in the god of their parents, but in something even bigger, if even at all. This is the impression I get from these lines. The writer is looking up into what he once believed was perforations in the sky, letting in light from heaven, as is an ancient belief, and realized a universe, "maybe more", was waiting on the other side. Whether this describes one person, or the whole of mankind does not matter at this point. It can be applied either way. Once this knowledge is known, it cannot be unknown. We leap ahead in understanding, and realize even deeper and more disturbing questions await.