This was capital offence — leader denied motive (6)
I believe the answer is:
reason
'motive' is the definition.
(I know that reason is a type of rational motive)
I don't understand the rest of the clue.
Can you help me to learn more?
(Other definitions for reason that I've seen before include "Explanation or justification" , "Logic and rationality" , "Capacity for rational thought" , "Motive; argue" , "issue" .)