Most stories are easy. 'Kill everyone that isn't you' is as far as most games go.
Occasionally there's a little motivation thrown in, stuff like 'they killed your father/girlfriend/puppy, now make them pay'.
But generally you're not going to find thought-provoking depths to analyze - obviously the auto-shotgun symbolizes the protagonist's growing sense of inadequacy. Every now and then, however, a game comes along with a script that feels like 20 people shouting at you all at once; a mess of sub-plots, timelines and twists that gives you an instant headache.
So consider this your one-stop cheat sheet to the hardest plots out there. All explained for you to understand with the minimum of pain. Oh, and there will be spoilers.