Plan to have precious stone beneath rock layers (9)
I believe the answer is:
stratagem
'plan' is the definition.
(stratagem is a kind of plan)
'precious stone beneath rock layers' is the wordplay.
'precious stone' becomes 'gem' (gem stone).
'beneath' means one lot of letters go next to another (in a down clue).
'rock layers' becomes 'strata' (I've seen this before).
'gem' after 'strata' is 'STRATAGEM'.
'to have' acts as a link.
(Other definitions for stratagem that I've seen before include "Start game with cunning plan" , "Devious ploy" , "Clever scheme" , "Cunning manoeuvre" , "A cunning plan or piece of trickery" .)