The Lyrics:
First, the lyrics of the theme are:
Big-O, Big-O o o Big-O,
Big-O, Big-O o o Big-O,
Cast in the Name of God,
You're Not Guilty,
We Have Danger,
Get Big-O
Refrain
It's in english too, even though it's the Japanese theme song. That's what's interesting. Go ahead, listen to it. That's what they're saying.
The Ending:
You know, I never actually considered that a possibility...
Spoilers:
I always thought they were all clones controlled by Angel, and the redux of the opening after the end credits of the final episode was their next copies. That's why they all lost their memories 40 years ago. They never had them to begin with.
But the Bigs, or Mega-Deus' were an allegory for the power of God, or more precisely, his army of angels. The ones that the villains had could have been an allegory for the Devil.
But the funny thing is that the way you explained it makes more sense...
(Oh great... Big-O The Musical...)