Clandestine faction assimilates religious teaching (6)
I believe the answer is:
secret
'clandestine' is the definition.
('secret' can be a synonym of 'clandestine')
'faction assimilates religious teaching' is the wordplay.
'faction' becomes 'sect' ('sect' can be a synonym of 'faction').
'assimilates' means one lot of letters goes inside another.
'religious teaching' becomes 're' (religious education).
'sect' placed around 're' is 'SECRET'.
(Other definitions for secret that I've seen before include "Unidentified" , "'Hidden, covert (6)'" , "Security classification level" , "Not seen or know by others" , "away from scrutiny" .)