Interesting post. I haven't read it through, but here's something that stood out to me:

Biology is something I personally suck at, even at the high school level. I can say the NHI look like the aliens from close encounters. As far as I know, we never had one alive. My source who told this was unsure if it was true or not. I didn't learn much about this wing, it's the most secretive. I do know its HQ is hidden in almost plain sight. I still feel like the guy who told me where it is had to be lying, because it was just too obvious. There are bodies stored in other locations apart from their main HQ.

Johns Hopkins? For some reason that name popped up to me when the OP mentioned "because it was just too obvious." Maybe I'm wrong though.