Working my way through Getting Started with Hypertext Narrative and it strikes me that separating Story from Plot means that, at the coarsest level, the layout of the story involves defining several plot lines, their cycles and identifying where and how they could interweave. Then using the various conditioning tools to determine what needs to happen before the plot lines can converge.
It also seems that starting from the end of the story - in my case, the completion of a successful project - and working backwards could help with determining Requirements.
Is that a fair summary? Or is it still too linear?