Something nasty afoot sees leader deserting alliance (5)
I believe the answer is:
union
'alliance' is the definition.
(I've seen this before)
I cannot understand how the remainder of the clue works.
Can you help me to learn more?
(Other definitions for union that I've seen before include "The joining of two or more together" , "Association - guild" , "(Pipe) coupling" , "junction" , "Merger like marriage" .)