Go in confused by commanding officer speaking softly (6)
I believe the answer is:
cooing
'speaking softly' is the definition.
(cooing is a kind of speaking softly)
'go in confused by commanding officer' is the wordplay.
'confused' indicates an anagram.
'by' means one lot of letters go next to another.
'commanding officer' becomes 'co'.
'go'+'in'='goin'
'goin' anagrammed gives 'oing'.
'oing' after 'co' is 'COOING'.
(Other definitions for cooing that I've seen before include "Making pigeon-like noises" , "Sounding like a dove" , "that'll go after billing?" , "Murmuring like a pigeon" .)