Basically, this is the afterlife. Things can be affected in this world in ways that the world of the living can't. You can make objects out of dirt if you have a good enough memory of them and you know how to assemble the parts. In the same way, someone used that ability to manipulate the environment to create a program that can basically alter the fabric of the afterlife. It's what made the NPCs.

[ Unless you're Naoi, but she's not going to get into that because she still doesn't necessarily get it. ]

So basically, they are designed to act like people.. but it's impossible to recreate a real person, so they're not actually people. They don't have real emotions, they'll forget wrongs if you stop doing them, they can be easily stuck into certain patterns so they're predictable. If a situation arises that the same system views as problematic, they turn into shadows and try to wipe us out by stripping us of our memories and personalities and turning us into one of them. Got it?