Pirate very shortly at sea in armed vessel (9)
I believe the answer is:
privateer
'armed vessel' is the definition.
(I've seen this before)
'pirate very shortly at sea' is the wordplay.
'shortly' means to remove the last letter.
'at sea' is an anagram indicator.
'pirate'+'very'='piratevery'
'piratevery' with its last letter taken off is 'piratever'.
'piratever' anagrammed gives 'PRIVATEER'.
'in' is the link.
(Other definitions for privateer that I've seen before include "Sailor may go on it" , "Drake, for example" , "Armed ship used in war but not government-owned" , "Non-government owned warship" , "Government-commissioned vessel authorised to prey on enemy shipping" .)