Mysterious vessel in time capsized (6)
I believe the answer is:
arcane
'mysterious' is the definition.
(I've seen this before)
'vessel in time capsized' is the wordplay.
'vessel' becomes 'can' (I've seen this before).
'in' is an insertion indicator.
'time' becomes 'era' (era is a kind of time).
'capsized' says the letters should be written in reverse.
'era' reversed gives 'are'.
'can' placed into 'are' is 'ARCANE'.
(Other definitions for arcane that I've seen before include "Requiring special knowledge" , "Esoteric, mysterious" , "Mysterious, secret or obscure" , "deep" , "Mysterious like a crane" .)