I'm calling in a tie on this one: Nyx (Resident Evil series) was honestly the freakiest thing I had ever seen in my life when I first encountered it, and it still measures quite high on the "Freakadelic Weirdometer."
Tied with Nyx is another pile of disembodied bits and pieces mashed together in a heinous blob: G. Even worse; I had to watch G go through all of his forms, slowly but surely becoming less human and more...I dunno, shoggoth? Whatever he was by the time I blew him clear into the next dimension, I was just glad he was finally gone...