Run through each deserter captured by the enemy (9)
I believe the answer is:
perforate
'run through' is the definition.
(thesaurus)
'each deserter captured by the enemy' is the wordplay.
'each' becomes 'per'.
'deserter' becomes 'rat' (I've seen this before).
'captured by' is an insertion indicator.
'the enemy' becomes 'foe' (I've seen this before).
'rat' inserted inside 'foe' is 'forate'.
'per'+'forate'='PERFORATE'
(Other definitions for perforate that I've seen before include "Make hole or holes through" , "Puncture" , "pass through hole" , "bore!" , "punch" .)