One of the things I force my students to pay attention to (some resist) is the concept of storyboarding out their science-based video game projects. But I know, from experience, how important it is to have a map forward, even if you abandon the map along the way for more creative terrain.
As a teacher, the storyboard also provides me with a way to see what they are thinking as they begin the design phase, as well as gives us discussion points on which to talk through the game design, science concepts and story ideas in a workshop-style mode.
You can read more about what I wrote about storyboarding, including the sharing of resources, over at the Gamestar Mechanic teacher site, from a few years ago.
Peace (in the boards),
Kevin