Cloud over boat moored in shelter (6)
I believe the answer is:
darken
'cloud over' is the definition.
(I've seen this in another clue)
'boat moored in shelter' is the wordplay.
'boat' becomes 'ark' (ark is a kind of boat).
'moored in' is an insertion indicator (inserted letters are held or moored in others).
'shelter' becomes 'den' (I've seen this in other clues).
'ark' placed into 'den' is 'DARKEN'.
(Other definitions for darken that I've seen before include "Grow less light" , "shade" , "Grow blacker" , "Dim" , "Make less light" .)