Get it here.

I put together a spreadsheet a little while ago that outlines what sort of encounters happen when, in what part of the story, who's involved, what type of encounter, etc. I basically just skimmed over the plot outlines to see what they mandated, and this is what came out. So please understand I'm providing this just to give us a place to start; I'm sure we'll make lots of revisions to this sort of information as we work on character abilities and challenges. (In fact, I'm posting this mostly to help out this task).

I broke the encounters up into three different types: puzzles, battles, and hybrids (a mix of puzzle-battle). Puzzles must be solved in order to advance the game. Battles have to be won (or otherwise finished to whatever state we require) to advance. Hybrids could be tackled either way, containing both puzzle elements and combat elements (or, puzzles with things to fight, if you want to put it that way).