Manuscript covering evil factories (5)
I believe the answer is:
mills
'factories' is the definition.
('mill' can be a synonym of 'factory')
'manuscript covering evil' is the wordplay.
'manuscript' becomes 'ms' ('ms' can be a synonym of 'manuscript').
'covering' is an insertion indicator.
'evil' becomes 'ill' (I've seen this in other clues).
'ms' enclosing 'ill' is 'MILLS'.
(Other definitions for mills that I've seen before include "Machines that grind or crush" , "See 7" , "Bomb" , "factories" , "''Among these dark Satanic ...'' (William Blake)" .)