I have a better grasp on it now. The story is going to be an Indiana Jones style adventure to a ruined city or temple to recover an ancient, semi-mythic artifact for the museum. There's one big puzzle I've already planned for the end, which will require some close reading of the story up to that point for clues, and then some smaller ones scattered throughout the trek there, navigating the ruins, etc. The big puzzle requires a fair bit of work with variables, which I haven't tried before, so that's the first thing I'm going to work on, and then whatever time / energy I have left after finals will be spent adding more little puzzles and adventures.