Down here, I see, is a deep dark sort of puzzle (5)
I believe the answer is:
crypt
This clue might be a double definition.
'down here i see is a deep dark sort' is the first definition.
Although both the answer and definition are singular nouns, I cannot see how one could define the other.
'puzzle' is the second definition.
The definition and answer can be both man-made objects as well as being singular nouns.
Perhaps they are linked in a way I don't understand?
'of' is the link.
Can you help me to learn more?
(Other definitions for crypt that I've seen before include "Burial vault" , "Church's basement" , "Underground burial chamber" , "Undeground room" , "Underground cell" .)