That's right, you don't separate subject from the predicate with a comma. (unless you've got some parenthetical-type construction.

Subj: something intrinsic to who Andy was

Pred: had been pierced and shattered

And then suddenly he realized that something intrinsic to who Andy was, late that night as the thunder caroomed off the trees resounding through the woods and the lightning bolts rent the sky like a Freddie gone amuck, had been pierced and shattered.

I just realized I have no idea how to spell that word. Reminds me of the time in grade school spelling contest when I was unable to spell "phlegm."