What if HE IS the Villain! Or well, a Character representing him.
Maybe someone built deep into the Lore as a "Shadow"-Character who has been everywhere, no matter which faction you join.
Someone who is friends with everyone, and noone.
A master of disguise, and yet he is showing himself to not cause suspicion on him.
He is your Family, your Friend, your Enemy and your Nightmare. You just haven't figured it out yet.