They all died because they had to leave their bodies behind. The next evolutionary step was to become one. No one alone, no one left behind. So they all died to become one spirit or being. Shinji was asked the decision if he wanted this and he said that with all the pain and so on he would rather be who he is so... Shinji and Asuka return to make a new world. The blood or pool seen is the primeval soup, its what starts life.