Yes, different indeed (3)
I believe the answer is:
aye
'indeed' is the definition.
(I've seen this before)
'yes different' is the wordplay.
I cannot quite see how this works, but
'yes' could be 'ay' and 'ay' is found within the answer.
A single letter 'e' remains which might be clued in a way I don't see.
This may be the basis of the clue (or it may be nonsense).
Can you help me to learn more?
(Other definitions for aye that I've seen before include "Word of assent" , "Yes (archaic)" , "Positive voting response" , "Yes; ever" , "One voting in favour" .)