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Ok, this is gonna sound stupid probably, but how on earth do you keep up with all the branches of a story without them getting tangled or lost in the mess. Especially when there are variables involved! I've been trying to write all the branches on a large piece of paper but I always run out of space or am like "wait, what if we add in a branch here instead" so much that it gets convoluted beyond use.

Photoshop (or any Paint program) is pretty useful.  Boxes and lines with arrows are pretty much all I need.

I mostly use OneNote, and then I try and draw out all the pathways. This program is useful since you can zoom in/out and extend the page length/width as needed. You can also easily erase or change pathways that you've decided to get rid of. Of course, any similar program should work just as well. It may be helpful to have a "master" page that shows all the major pathways in your story, and then alternative pages to show the smaller branches within any particular chapter. 

Edit: I've also kept a master list of all variables on a separate page (not accessible with any links) on the first chapter of my story. They are sorted and labeled by the chapter in which they are found. It helps me remember what everything does, which is really useful with larger works that you might be working on over long periods of time (especially when debugging). Then, within each chapter of my story, I have a "Loose Links" / "Debugging" page which reminds me of modifications that need to be made within the chapter, variables that need to be modified, etc. 

I've tried several mind mapping sites but have yet to find anything simpler and more straightforward than MSPaint.

Always on the look out for something classier though. The company that makes Scrivener has another program called Scapple that looks promising, but it's a pay thing.


Sometimes I skip the mapping stage altogether though and just start writing some fat paragraphs about plots and possibilities.