To understand it fully: Humanity committed a great sin when they tried to create God by experimenting on Adam, thus the Second Impact occured. Human souls were no longer in great supply after mankind sinned so greatly. So, in a way, humanity had to restart itself, which is the human instrumentality project. The goal is to combine all of humanity into one body, just like the Angels. This body is Rei for those who didn't figure her role out. Seele wishes to combine all of humanity for absolute happiness, and Shinji is the only one who actually seems to be able to do it, because only he can pilot Unit-01. All that fucked up shit with the Eva series happens, and Unit-01 is crucified and Shinji becomes a temporary God. Shinji decides, after finally gaining enough balls to make a decision by himself, that humanity should not be one. Thus, All humanity is liquified except him and Asuka, in essence becoming a new Adam and Eve.