Murder in the Spanish Main - it upset pirate, ultimately (9)
I believe the answer is:
eliminate
'murder' is the definition.
(thesaurus)
'the spanish main? it upset pirate ultimately' is the wordplay.
'the spanish' becomes 'el'.
'upset' indicates anagramming the letters.
'ultimately' says to take the final letters.
The last letter of 'pirate' is 'e'.
'main'+'it'='mainit'
'mainit' is an anagram of 'iminat'.
'el'+'iminat'+'e'='ELIMINATE'
'in' acts as a link.
(Other definitions for eliminate that I've seen before include "Take out" , "put out" , "defeat" , "Exclude from further stage of competition" , "Wipe out" .)