Short answer: They are aliens, presumably anyways.
Long answer: Their true form is that of a seemly mindless giant flesh-eating black blob monstrosity. Presumably, the scientists at that institution was able to put them into canisters and insert them into the spinal cords of human girls (there's probably a reason why its all girls). Due to this, they were able to from some kind of connection with the brains of the host, copy the brain and emulate it. They then replace the host's brain and act as the brain of the host's body. While emulating the host's brain, they act like any normal human in pretty much every way, unaware of their true nature the same way how we knew little to nothing about our own brains until the advent of neuroscience. When they "hatch," they revert back to their true form of a man-eating abomination but it seems they still retain some of the memories of when they were still emulating a human brain.
An important point to note is that the identity associated with the "drasil brain" is distinct from that of the original host's brain. This is why when Neko "awoken" during her fight with Mako she seemed like a completely different personality, because she most likely is. The amnesic sweet Neko we see for most of the story is the "Drasil Neko" and the brash one who fought Mako is the original Neko, Murakami's childhood friend.
My assumption on why Drasil Neko loses her memories when she uses her power is because her drasil brain overexerts itself when using its powers, causing something similar to brain damage, which results in memory lost. I also assume that the reason why the original Neko resurfaces when Drasil Neko releases her full power is because in order to use her full powers, she has to suspend her ability to act as brain, allowing the original's brain to resurface.
I read somewhere in the manga that the drasil actually eats the host's original brain, or at least part of it, and uses that as the basis for emulating a human brain but I'm not too sure.
As for the ending, given what I said, it will probably not be a very happy ending. I can think of 5 possible endings:
1) Murakami ends up having to kill them all because they've reverted back to their true hideous nature or in order to prevent them from doing so. He endeavors to come to terms with it and moves on. Bittersweet farewells.
2) They come to term with their monster nature and leave the host bodies, going back to where they came from. The host bodies are either returned to the original ownersor are left for dead. Bittersweet farewells.
3) The girls sacrifice themselves and return the bodies to the original owners. Bittersweet farewells.
4) The original host's brains are gone and cannot be recovered. They find a way to permanently incorporate the drasil brains into the host bodies and the girls can finally try to live as normal girls. I would say bittersweet farewells to the original owners but we've never even met the originals except a few scenes with the original Neko so it probably won't be that sad.
5) The original's brains are incorporated into the drasil brain and the girls learn to coexist inside the same body.
Edited by KaazaLite, 01 January 2015 - 01:01 PM.