I use Google Docs primarily as it has the best collaboration tools and it loads easiest on the Android tablet I sometimes write on. It does make things complicated if you are branching a lot though, so I use the visual TWINE editor if its meant to.
Oddly enough I've found that that Diagrams.net is great for keeping track of branching episodes. There was a bit of a learning curve, but I was able to build out a flowchart for a story I did on another website that doesn't have any way of visualizing branching stories. When you expand each rectangle it shows the chapter and my chapter notes. I wouldn't necessarily write a chapter using Diagrams, but it's a nice tool to keep track of long branching stories.