Opening and middle sections of final fugue really used in alternation (9)
I believe the answer is:
inaugural
'opening' is the definition.
('inaugural' can be similar in meaning to 'opening')
'in alternation' is the wordplay.
'alternation' becomes 'augural' (I can't justify this - if you can you should give a lot more credence to this answer).
'in'+'augural'='INAUGURAL'
'and middle sections of final fugue really used' is the link.
This may not be right. Some or all of it may be part of another bit of the clue.
Can you help me to learn more?
(Other definitions for inaugural that I've seen before include "Relating to start of job or course" , "It may be delivered" , "Of a speech made on taking office" , "Marking the beginning of, eg, an institution" , "First address" .)