Deer, initially not headless, reproduced, stood still (9)
I believe the answer is:
stagnated
'stood still' is the definition.
(I've seen this before)
'deer initially not headless reproduced' is the wordplay.
'deer' becomes 'stag' (stag is a kind of deer).
'initially' indicates taking the first letters.
'headless' means to remove the first letter.
'reproduced' becomes 'mated'.
The first letter of 'not' is 'n'.
'mated' with its initial letter taken away is 'ated'.
'stag'+'n'+'ated'='STAGNATED'
(Other definitions for stagnated that I've seen before include "Vegetated" , "Stood still" , "progressed no further" , "made no progress" .)