Imagine not having an Independent cryptic puzzle! (6)
I believe the answer is:
enigma
'puzzle' is the definition.
(I've seen this before)
'imagine not having an independent cryptic' is the wordplay.
'not having' suggests deleting specific letters.
'an independent' becomes 'i'.
'cryptic' indicates an anagram (a cryptic or obscure order of the letters).
'imagine' with 'i' taken out is 'magine'.
'magine' is an anagram of 'ENIGMA'.
(Other definitions for enigma that I've seen before include "Conundrum" , "Puzzle for gaming" , "Gamine being a bit of a puzzle" , "There's a mystery in game" , "WW two Ger. code device; puzzle" .)