Mankind has already come to the dead-end on its present state of evolution. To save mankind from extinction, "Human Instrumentality Program" is being executed. It is a process to artificially evolve mankind to a higher state of existence, the way to exist without mortal bodies, and to exist as a perfect single being.

To achieve this, it is necessary to artificially create the "Fruit of Life" from the "Tree of Life", something owned by God and forbidden to be touched by mankind. Here's where Evangelion come in. EVA-01 has the most important role in this artificial making of the "Tree of Life", that's why Gendou forbid it to be used after EVA-01 ate Angel#14. EVA-01 has become a "god-like" entity once it ate the Angel and gain S2 Engine naturally. (S2 Engine = Super Solenoid Engine; EVAs with S2 Engine don't require the umbilical cable to function).

Finally, "Third Impact" must be initiated to destroy the material world and to complete the process. Although both SEELE and Gendou wants Third Impact to happen, they believe that by controlling the Third Impact, by being the one to first return to Lilith without losing one's physical body, is thought that one will gain power of some sort. That's why Keel tries to destroy NERV, after the last Angel was eliminated - he wants to have the ultimate power.

The true key to the program is actually Lilith and the Longinus Spear that is stabbed into her heart. They are both hidden inside the "Terminal Dogma" waiting for the "Human Instrumentality Program" to be initiated. Lilith's face is covered by a mask in the shape of "God's Seven Eyes". The Longinus Spear is pierced into her heart to prevent her from growing completely. (Note: Longinus is the Roman soldier who pierced the heart of Christ)