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