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Question.  Do you just make up the story as you go. Or do you make a sort of notes and what not of where you want to go with the game and story?

Judging by his past posts and my past experiences as a DM for D&D, i'd say he had a rough outline for most of the story, mostly consisting of big events and themes for each of the acts. Its likely vague at first, allowing for the evolution of the story as new ideas come. As development catches up to the outline, things are solidified and flushed out in more detail.

Pretty much what Diadita said :)

I already have all the major story beats that the game has to hit planned out, as well as the endings and any large set pieces. Apart from that I keep only a vague outline so that the characters have room to evolve organically and I can respond to player feedback to tweak things that aren't working, or add things that people request.