Come of think of it, there was actually a book I read that was more or less on this subject some years back called Creating Emotion in Games: The Craft and Art of Emotioneering by David E. Freeman. It’s apparently out of print now, but there are some really cheap used copies on amazon. As with everything, your mileage may vary on it’s usefulness, and some of it’s references are definitely “dated” to a degree, but the basic premises should be the same. He includes some “rules” and “systems” for writing interesting characters and structuring plots specifically for games, as well as writing dialogue and the like. It’s not the same thing as a “pipeline” like you’ll see for other assets, but it does provide some guidance from a semi-academic standpoint.
There was also the Art of Game Design by Jesse Schell](http://www.amazon.com/Art-Game-Design-Lenses-Second/dp/1466598646/ref=sr_1_1?s=books&ie=UTF8&qid=1459490979&sr=1-1&keywords=Jesse+Schell), which IS still in print, though it’s not cheap. It’s vastly more general purpose, but some of it applies to story design as well, though quite a bit less then the first book.
There was a third I kind of read as well about interactive storytelling, but I cant remember it’s name off the top of my head, just that I had some fairly fundamental philosophical differences with it’s author on the subject to the point I’d just toss it down in mild annoyance every time I tried to read it.