to me, it always sounded like a description of a trip. the "doctor" is the guy who gave him the acid. the opening lyrics are just the images and thoughts he's experiencing ("gold is lead" is obviously a reference to alchemy, and I never thought anything of it beyond that). the middle, lyrics-free section is him experiencing the rest of the trip. he sets it up to make it sound as if it's a bad one, but then at the end he has an epiphony ("I'm alive/flowers thirve/realise!"). I don't know how valid that is, but it was just always my take on it.
to me, it always sounded like a description of a trip. the "doctor" is the guy who gave him the acid. the opening lyrics are just the images and thoughts he's experiencing ("gold is lead" is obviously a reference to alchemy, and I never thought anything of it beyond that). the middle, lyrics-free section is him experiencing the rest of the trip. he sets it up to make it sound as if it's a bad one, but then at the end he has an epiphony ("I'm alive/flowers thirve/realise!"). I don't know how valid that is, but it was just always my take on it.