@pelletboy: @WestboundRobN: The physical form of the Human Instrumentality Program is more clearly seen in the End of Evangelion movie, but through it, the final episode of the series can be explained as well. All living things are made of LCL, the fluid in the plug units that serve as cockpits for Evas, the blood of the Angel Lilith. Instrumentality, through the awakening of both Eva Unit 1 and Rei Ayanami tears away the weak AT-fields that all people have which allows them to maintain their physical forms, turning the world into a large sea of LCL.
This sea has only a single consciousness, no Ego. What Shinji in the final episode goes through is his psyche coming to accept instrumentality, giving up its sense of self, and embracing whatever ideal world the grand consciousness of the sea of LCL will engulf him in. That final scene where everyone he knows is standing there congratulating him is him achieving instrumentality, and all of what use to be humanity welcoming him into the fold.
End of Evangelion's ending however has Shinji refusing instrumentality. We are not privy to as much of his personal psyche in this version, but we do see him regaining human form, his Ego being powerful enough. The only other character within the show with such a powerful ego is Asuka, hence why they are ultimately alone in this sea of LCL.