Sheltered in a bower he had outside (9)
I believe the answer is:
harboured
'sheltered' is the definition.
(harbouring is a kind of sheltering)
'bower he had outside' is the wordplay.
'bower' becomes 'arbour' (synonyms).
'he had' becomes 'he'd'.
'outside' is an insertion indicator (some letters go outside others).
'arbour' inserted within 'hed' is 'HARBOURED'.
'in a' is the link.
(Other definitions for harboured that I've seen before include "Sheltered" , "found shelter" , "concealed" .)