Ship stored rye at sea (9)
I believe the answer is:
destroyer
'ship' is the definition.
(destroyer is a kind of ship)
'stored rye at sea' is the wordplay.
'at sea' indicates an anagram.
'stored'+'rye'='storedrye'
'storedrye' anagrammed gives 'DESTROYER'.
(Other definitions for destroyer that I've seen before include "Apollyon's" , "One scuppers" , "HMS" , "Apollyon maybe" , "Small, fast warship" .)