Commander-in-chief with an orange missile at sea (13)
I believe the answer is:
generalissimo
'commander-in-chief' is the definition.
(I've seen this before)
'with an orange missile at sea' is the wordplay.
'with' means one lot of letters go next to another.
'at sea' is an anagram indicator.
'orange' put next to 'missile' is 'orangemissile'.
'orangemissile' with letters rearranged gives 'GENERALISSIMO'.
(Other definitions for generalissimo that I've seen before include "Supreme commander (It.), title used by Franco" , "Political and military leader" , "Supreme commander of combined military forces" , "Commander in chief" , "Commander-in-chief" .)