Puzzled? Ponder in the course of plot (7)
I believe the answer is:
bemused
'puzzled?' is the definition.
(being bemused is being puzzled or confused)
'ponder in the course of plot' is the wordplay.
'ponder' becomes 'muse' (synonyms).
'in the course of' means one lot of letters goes inside another.
'plot' becomes 'bed' (bed is a kind of plot).
'muse' placed inside 'bed' is 'BEMUSED'.
(Other definitions for bemused that I've seen before include "Floored" , "Puzzled" , "Perplexed or absorbed in thought" , "Perplexed, bewildered" , "Dazed" .)