Precious stones beneath rock layers in plots (10)
I believe the answer is:
stratagems
'plots' is the definition.
'precious stones beneath rock layers' is the wordplay.
'precious stones' becomes 'gems' (gem is a kind of precious stone).
'beneath' means one lot of letters go next to another (in a down clue).
'rock layers' becomes 'strata' (I've seen this before).
'gems' after 'strata' is 'STRATAGEMS'.
'in' acts as a link.
(Other definitions for stratagems that I've seen before include "Plans" , "Manoeuvres" .)