Need help interpreting these lyrics (Past the Mission - Tori Amos/Trent Reznor)

This woman (Tori Amos), sometimes, her lyrics are ridiculously hard figure out. She’s a true talent and a one of a kind musical artist.

This song, Past the Mission, what does it mean:

I don’t believe I went too far
I said I was willing
she said she knew what my books did not
I thought she knew what’s up

Past the mission
behind the prison tower
past the mission
I once knew a hot girl
past the mission
they’re closing every hour
past the mission
I smell the roses

She said they all think they know him well
she knew him better
everyone wanted something from him
I did too but I shut my mouth
he just gave me a smile

Hey they found a body
not sure it was his
still they’re using his name
and she gave him shelter
and somewhere I know she knows
somewhere I know she knows
somethings only she knows

(favorite song at the moment)