Lyric discussion by Ex Abrupto 

As you said this is obviously about the religion. I would also add my personal theory about Rudy ( yes the Rudy from the Crime of the Century song ). I believe that some Supertramp songs are about Rudy and this one is probably about him as well. Chronogically speaking I would put it right after " Hide in your shell ". Rudy, after suffering something real bad, comes back to where he spent time as a child: church and his bitter taste of life now shows him things he did not realize back then. He does not find the comfort he searches for and he turns even more bitter and the " downward spiral " commences.

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