Submarine captain turns up with small signs (5)
I believe the answer is:
omens
'signs' is the definition.
(I know this)
'submarine captain turns up with small' is the wordplay.
'submarine captain' becomes 'nemo' (character from 20,000 Leagues Under the Sea).
'turns up' shows that the letters should be reversed in order.
'with' is a charade indicator (letters next to each other).
'small' becomes 's' (abbreviation - e.g. clothes size).
'nemo' written backwards gives 'omen'.
'omen'+'s'='OMENS'
(Other definitions for omens that I've seen before include "Signs of things to come" , "Portents, prophetic signs" , "Auguries" , "Prophetic signs of good or evil" , "Augurs" .)