Stop and take a breather after a run (6)
I believe the answer is:
arrest
'stop' is the definition.
('arrest' can be a synonym of 'stop')
'take a breather after a run' is the wordplay.
'take a breather' becomes 'rest' ('rest' can be a synonym of 'take a breather').
'after' says to put letters next to each other.
'a run' becomes 'ar' (I've seen this in other clues).
'rest' put after 'ar' is 'ARREST'.
'and' acts as a link.
(Other definitions for arrest that I've seen before include "Take into legal custody" , "Land next to the sea" , "Cause to stop" , "Stop (on suspicion)" , "Sartre (anag) -- check" .)