A common writing tool is to use a story grid. You have chapters/similar along the Y axis and title, characters, plot elements, etc. along the X axis. That way you can keep track of what information you are revealing at each story beat/chapter, make sure that plot twists work (e.g. when outlining something like The Sixth Sense).

Depending on how big the story is and how many characters/plot threads there are, I can see the Excel files getting large.