When we wrote the story for our first Choose Your Own Adventure game we used the classic three-act story arc structure to figure out the broad plot points we wanted, and then built up from there. So we had our beginning (establish the player's purpose and humble origins, and then start to build them up towards something good), the middle (player comes close to initially achieving dreams/goals, but then suffers major adversity and is set back), and then the end (player overcomes adversity and builds themselves back up to achieve the goals they missed out on previously).
Within each act we then identified smaller plot points we wanted to explore, additional characters to introduce, and threw in a few crazy ideas for fun. We weren't getting into detailed story/script writing for a month or two until we'd figured out the over-arching structure and were happy with it.
Once you get to the detail step you might like to check out http://twinery.org/ if you don't already know about it; it's a really great tool for visualizing interactive stories with tons of different parts.
Best of luck with your project!