is great for flowcharts. You can even connect it to Google Drive and have your stuff online. IDK if you can easily insert pictures, you probably can. It's fantastic for writing down branching storylines and even including the conditions that lead to it.
As far as writing and organizing a lengthy story, just using a text processor like Word is good enough. If you create an index for each chapter, you can navigate it easily. It might not be so great if you have branching, but if you carefully index your quasi-chapters, you could reference them (at least symbolically by name) from your flowchart. That way you can have the flowchart for organization and the document for details. IDK if you can even link them together in some way.