Welcome @eyabaa!
Thanks for this post. I appreciate new creative ways for note taking.
I also like reusing existing tools. Below is an attempt to organise notes in Story Mode, using to-do notes as chapters, linking them to one another (including branching), and visualising the result in a note folder (on the left, the closest I had to a progress bar) and a note graph (on the right, using this plugin). Would that work in your opinion? What features are missing from this "mode"? (Maybe they could be implemented as a small plugin.)