His Excellency's in ultimate command (6)
I believe the answer is:
behest
'command' is the definition.
(I know that behest is a type of command)
'his excellency's in ultimate' is the wordplay.
'his excellency' becomes 'HE' (abbreviation).
'in' indicates putting letters inside.
'ultimate' becomes 'best'.
'he' inserted into 'best' is 'BEHEST'.
(Other definitions for behest that I've seen before include "Command, bidding" , "(At someone's) command" , "Order" , "Command - Thebes (anag)" .)