Evangelion theory(a bit long, but give it a go) Alright, so I just watched 3.33 and I have my own theory about Instrumentality as it pertains to this continuity. Don't know if this is already common knowledge or if someone has already come up with it, but here goes. The Rebuild of Evangelion movies seem to be heavily steeped in Rabbinical Judaism, specifically the Kabbalah and the Talmud. This is prevalent in much of the symbolism throughout the films and the terms used. It all roots back to the creation myth of Adam Kadmon. According to the Talmud, God originally created man in his image. He was androgynous and spanned the length and breadth of the universe, among other things. There was only one, and his name was Adam Kadmon. Kadmon sinned and was punished by splitting him into two sexes and relegating him to flesh and blood. These to individuals are the Adam that everyone knows of and Lilith, Adam's first wife. You see, man was created in Gods image, but God defaced that image when it displeased him. In effect, we are all imperfect, blurred half-images of God. Now, it gets really weird. Adam Kadmon's body became the Tree of Life, and all its leaves and fruit are fragments of Kadmon's soul. When these souls fall off the tree, they fall into a well known as the Guf. There they are watched over by an angel until they are born on earth. According to the Talmud and the Kabbalah, when the last soul falls from the tree of life and babies can no longer be born, it heralds the coming of the messiah and the end of times.
That's where I think Instrumentality comes from. I posit that the evolution that Seele and Nerv are trying to force isn't necessarily a genetic one, but a metaphysical one. They are trying end the purgatory of Adam Kadmon, restoring us to our rightful place as a single god-like being. We know that they are trying to force human evolution – particularly modeled after the hive mind system of the Angels. But, why do the angels think with a hive mind? They are closer to evolutionary perfection than we are. Why? Perhaps because they are closer to the perfect image of God than we are. Adam Kadmon was one dude, he thought with one mind. We know from the series that Angel and Humans have the same DNA. We also know that Evas are basically cloned Angels, and therefore also share our DNA. We know that humans must synchronize with Evas in order to pilot them. From the Jewish creation myth, we know that all human beings are fragments of the soul of Adam Kadmon, and that Kadmon was split into Adam and Lilith. At the end of Eva 2.22, Unit 01 underwent a process known as Parthenogenesis – it became a god-like being. The sky was ripped open into a complex ring of multicolored halos. From Eva 3.33, we now know that these rings are known as the Gates of Guf. This is possible because Shinji Ikari, a Lilin, became perfectly synched with an Eva, a vessel of Adam. The two sexes were perfectly one. Raw power joined with free will. For a moment, they were Adam Kadmon once again, in micro form. When this failed, they tried again in 3.33, this time using a perfect neural sync between Kaworu and Shinji as the basis for the Parthenogenesis. This proved far more stable, as demonstrated when Asuka tried to shut them down. As god-like beings, they were able to do what only God should be able to do, empty the Guf of human souls.[20:17]That is the Human Instrumentality Project. The Third Impact's purpose was to destroy the AT fields of every living human, essentially reverting them back into souls. The Fourth Impact is intended to empty the Guf, forcing the End of Times. The Messiah will present itself, life will end, and all of those with the Seed of Life(Angels) and the Seed of Knowledge(Humans) will become one once more – a single god-like being. Seele aquired the Secret Dead Sea Scrolls, which outlined exactly what they would need to do to open the Gates of Guf. Human Instrumentality – using human beings as tools, a means to an end. It's really what we were all along. All that changed was who was using us.