Well, it took some searching but I found the story design docs I did that I need to progress. I'll worry about the player/enemy interaction issues that I wrote about yesterday later on; it will make more sense in the context of a greater overarching story sequence, anyhow.
The first stage in implementing this story is to put in the "blue doors". These represent your links to the real, real world, and also play into the system of upgrading your guns, so once they are in I will probably put the system in place that you need in order to get your guns. There won't be much in the way of obstacles to do this, but I can at least put the basic sequences in that you have to walk through in order to get your weapons. This represents effectively the backbone of gameplay progression.