Seriously, I'm convinced that Square didn't actually write a story for the game. This is what I think happened: all of the writers sat down in a meeting and one says "Okay, let's brainstorm a list of really cool events and plot twists that we could use, then we'll pick the best ones and build the plot from there." Only, instead of doing exactly that, they just kept everything on the list and mashed it together into a TERRIBLE game. The whole thing was just a mishmash of unrelated events and random crap. Eye candy, nothing more.
Threaded Mode