Plot contains treasure under layers of rock (9)
I believe the answer is:
Here is my best explanation:
'plot' is the definition.
'treasure under layers of rock' is the subsidiary indication.
'treasure' becomes 'gem' (gem is a kind of treasure).
'under' says to put letters next to each other.
'layers of rock' becomes 'strata' (I've seen this in other clues).
'gem' put after 'strata' is 'stratagem'.
'contains' is the link.
(Other definitions for stratagem that I've seen before include "Ploy - start game (anag)", "Cunning plot", "Plan to deceive enemy", "A cunning plan or piece of trickery", "could be a trick", "Clever scheme", "Manoeuvre - Ma's target (anag)", "Device", "Scheme to outwit an opponent" and "Ruse".)