Shogun is only going to accept complete agreement (6)
I believe the answer is:
unison
'complete agreement' is the definition.
(unison can mean total agreement or harmony)
'shogun is only going to accept' is the wordplay.
'to accept' says the answer is hidden in the clue.
'UNISON' can be found hidden inside 'shogun is only going'.
(Other definitions for unison that I've seen before include "Unscrupulous dealer" , "Sameness in pitch" , "The concordant trade union?" , "A coincidence of musical notes" , "All singing the same notes" .)