Exercise affected aliens' discipline (8)
I believe the answer is:
penalise
'discipline' is the definition.
('discipline'->'penalize' is in my internal thesaurus and 'ize'->'ise')
'exercise affected aliens'' is the wordplay.
'exercise' becomes 'pe' (Physical Education).
'affected' is an anagram indicator.
'aliens' is an anagram of 'nalise'.
'pe'+'nalise'='PENALISE'
(Other definitions for penalise that I've seen before include "Disadvantage unfairly" , "See plain (anag.)" , "Perhaps, fine" , "Inflict punishment on" .)