The Human Instrumentality Project

The End of Evangelion - and a new beginning

The tools needed to accomplish this goal would be Lilith, Adam, and the Lance of Longinus. As replacement for Lilith, EVA-01 would work, as she was cloned from Lilith (unlike all other EVA's that were cloned from Adam). SEELE also had planned to replace the Longinus Lance with the replica's their MPU's were carrying.
But all planning was finally obsoleted, when Gendo's accomplishing-tool (Rei) chose to lay mankind's future in Shinji's hands. And neither did Shinji choose to unite mankind (because he didn't want to loose his individuality), nor to create a world without people hurting each other, but a world without people hurting each other.
As sole survivors of Third Impact, he chose himself and Asuka, they remained on a dead, lonely world with red oceans of LCL - although it was said that every human being would achieve the ability to recreate it's own form though it's AT-field and could be born again.
This is what End of Evangelion portrayed as the end to the story, in the TV-episodes 25 and 26, it seems that Shinji chose a world without people hurting (!) each other .