Lyric discussion by treant 

Let's suppose the rain is a metaphor for war.

Long as I remember the rain been comin' down
Clouds of mystery pourin' confusion on the ground.

Wars have happened throughout history, leaving chaos in their wake.

Good men through the ages tryin' to find the sun.
And I wonder still I wonder who'll stop the rain.

For ages people have been trying to find "the sun" -- peace, enlightenment, utopia -- but who will stop the violence that always seems to emerge?

I went down Virginia seekin' shelter from the storm

The narrator goes to Washington, D.C. (adjacent to Virginia) looking for solutions to war, but instead gets caught up in "fables" while watching the "tower" of government grow further from the people.

Five year plans and new deals wrapped in golden chains.
And I wonder still I wonder who'll stop the rain.

The "five year plans" were a series of Soviet development programs laid out by Stalin, while the "New Deal" was a set of federal programs and reforms enacted by FDR. But the promises of peace and prosperity were "wrapped in golden chains", suggesting that they had hidden costs to freedom.

Heard the singers playin', how we cheered for more.
The crowd had rushed together tryin' to keep warm.
Still the rain kept pourin', fallin' on my ears
And I wonder, still I wonder who'll stop the rain.

This is a description of a scene at Woodstock that inspired the song. The overall image is of a large number of people coming together with shared ideals of peace and freedom. But despite the songs and cheering crowd, the Vietnam War continued unabated in the background, leaving the singer wondering who would be able to truly bring an end to war.

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