Done with gun: rotting in prison (7)
I believe the answer is:
dungeon
'prison' is the definition.
(a dungeon is a prison cell)
'done with gun rotting' is the wordplay.
'with' means one lot of letters go next to another.
'rotting' indicates anagramming the letters.
'done' put after 'gun' is 'gundone'.
'gundone' is an anagram of 'DUNGEON'.
'in' is the link.
(Other definitions for dungeon that I've seen before include "Eg, the Black Hole of Calcutta" , "Prison cell, often underground" , "Unpleasant cell" , "part of prison" , "Dark underground cell for prisoners" .)