Underlying reason (9)
'underlying reason' is the definition.
(I've seen this in another clue)
This is the entire clue.
(Other definitions for rationale that I've seen before include "Logic, reasoning" , "explanation" , "grounds?" , "Underlying principle" , "Why regulate" .)
(Other definitions for root cause that I've seen before include "Fundamental reason" , "The origin of a problem" .)