Bomb nuclear reactor broken by nearly-new software (9)
I believe the answer is:
pineapple
'bomb' is the definition.
(I've seen this before)
'nuclear reactor broken by nearly-new software' is the wordplay.
'nuclear reactor' becomes 'pile' (pile is a kind of nuclear reactor).
'broken by' is an insertion indicator (inserted letters break into the word).
'nearly' means to remove the last letter.
'software' becomes 'app' (I've seen this before).
'new' with its final letter taken off is 'ne'.
'ne'+'app'='neapp'
'pile' enclosing 'neapp' is 'PINEAPPLE'.
(Other definitions for pineapple that I've seen before include "that might go off?" , "Large juicy tropical fruit, or a grenade" , "Fruit grown on ground" , "Fruit (tree and fruit!)" , "Juicy tropical fruit or slang hand grenade" .)