Small church shelters border plot (6)
I believe the answer is:
scheme
'plot' is the definition.
(scheming is a kind of plotting)
'small church shelters border' is the wordplay.
'small' becomes 's' (abbreviation - e.g. clothes size).
'church' becomes 'CE' (abbreviation for Church of England).
'shelters' is an insertion indicator.
'border' becomes 'hem' (I've seen this before).
'ce' going around 'hem' is 'cheme'.
's'+'cheme'='SCHEME'
(Other definitions for scheme that I've seen before include "Lay plans" , "Systematic plan or arrangement" , "Plan (maybe best laid?)" , "Work out a course of action" , "Hatch - plot" .)