You've gone off topic, This is about which game out of Twilight Princess or Majora's Mask is darker...not which one you think is the darkest out of the series ;).
Your not thinking deep enough into it....the people that lived in the Twilight while surrounded by the Shadow Beasts thought they were in a living hell pretty much, An example being the citizens of Kakariko when they are hiding out in the Shaman's house, Another being the guy that gives you the...
If I remember correctly she didn't know where her father was, I don't think she was looking after him. I think he was experimenting on something and got stuck in some sort of closet, I can't remember what it was he got stuck in though.
I don't know really...come to think of it I think that both...