Lyric discussion by foreverdrone 

My intuition is that he's singing about a woman he once loved who is having terrible problems with mental illness, and is perhaps confined to an institution.

("...we passed through the hallway of shatterproof glass..." i.e. they can see but they can't touch. The glass imprisons those on one side, while on the other side it protects the "normal" world from being "infected" by insanity)

He desperately wishes he could do something to help, but fears that if he gets too involved with her, his own mental state will succumb to the same downward spiral.

Bob only knows what "goldheart mountaintop queen directory" means. It could be an example of the kind of (apparently?) meaningless "word salad" spoken by people who are schizophrenic or who have brain damage.

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