Capacity for rational thought (9)
'capacity for rational thought' is the definition.
(I've seen this before)
This is the entire clue.
(Other definitions for reason that I've seen before include "Logic and rationality" , "'Motivation, grounds (6)'" , "Explanation or justification" , "Think in a logical way" , "Logic of senora" .)
(Other definitions for intellect that I've seen before include "Mental powers; clever person" , "Mental power" , "Cognitive faculty" , "Reason" , "Brain" .)