Yeah, I don't think Section 31 and the concept of it would be too hard to grasp for the non-Trek audience really or wind into a story.
It's involvement is possible but unlikely for a TOS based story.
'If the Apocalypse starts, beep me!' - Buffy Summers
'The sky's the limit.....' Jean-Luc Picard, 'All Good Things'
courtesy of Saquist