Sets up secret organisation (6)
I believe the answer is:
erects
'sets up' is the definition.
('erect' can be a synonym of 'set up')
'secret organisation' is the wordplay.
'organisation' indicates an anagram.
'secret' anagrammed gives 'ERECTS'.
(Other definitions for erects that I've seen before include "Puts up, builds" , "Puts up, stand or building" , "Sets up or builds." , "Builds, constructs" , "Raises" .)