It's puzzling how gin and it came to be ordered (9)
I believe the answer is:
enigmatic
'it's puzzling' is the definition.
(synonyms)
'gin and it came to be ordered' is the wordplay.
'and' says to put letters next to each other.
'to be ordered' indicates an anagram.
'it'+'came'='itcame'
'gin' put after 'itcame' is 'itcamegin'.
'itcamegin' anagrammed gives 'ENIGMATIC'.
'how' is the link.
(Other definitions for enigmatic that I've seen before include "Puzzling, like the Sphinx" , "Cryptic, mysterious" , "not obvious" , "Mysterious or puzzling, like Mona Lisa's smile" , "Hard to fathom" .)