Human Instrumentality Project

The Human Instrumentality Project (人類補完計画, Jinrui Hokan Keikaku) is SEELE's secret goal: the forced evolution of humanity through bringing about Third Impact under their own control. The Human Instrumentality Committee oversees NERV's work to bring about completion of the project.

Basics of Instrumentality
As a result of Third Impact, all Lilin souls would be gathered into Lilith's Egg and united as one being. This would create transcendental abstract levels of existence where nobody existed singularly, but merely as part of the whole. In Instrumentality, the flaws in every living being would be complemented by the strengths in others, thus erasing the insecurities in people's hearts. They want to awaken Lilith to trigger the Third Impact and thus to bring the Chamber of Guf to unite all people and to create a transcendental abstract level of existence because only Lilith has the power to create, affect, or destroy the abstract transcendental levels of existence.

SEELE's Plans
While the above explanation is given repeatedly throughout the series and The End of Evangelion, a scene in the latter suggests there is more to SEELE's plan for Instrumentality. A SEELE member mentions during a conference that they do not need to set aside their human forms to use Evangelion as their "own private ark", which seems to contradict the plan of all humans losing their individual forms. The exact meaning of this is not given, and SEELE appears to embrace the Rei-and-Shinji-controlled Instrumentality at the end of the film.

However, SEELE's objectives are greatly expanded upon in the game Neon Genesis Evangelion 2. The Classified Information and the SEELE ending of the game discuss a very different form of Instrumentality than seen in the series - SEELE intended for Instrumentality to only be for their own council members. Rather than forming a sea of LCL, SEELE wishes to be merged inside an Evangelion unit with its own S², after destroying the Spear of Longinus. By placing their own souls within the body of a godlike being, and destroying the only weapon that can harm the body, they would effectively create an immortal God with a human soul which would represent the pinnacle of human existence, and live through all of eternity.

SEELE's plan as presented in the game is unconcerned with the rest of humanity. While the council members are to be joined in the Godlike being, all other humans will cease to exist.

Gendo's plans
Gendo allows SEELE to believe he is following their plan, but actually sticks to his own: he wishes to use Instrumentality to reunite with his wife Yui; while he mentions to SEELE that "death creates nothing", the series never goes into more detail on what plans he had for the rest of humanity during Instrumentality.

In the Neon Genesis Evangelion 2 game, Gendo's plan culminates with all souls merging inside Unit-01. Gendo, and Shinji, are at last reunited with Yui.