The Human Instrumentality Project, propelled with utmost secrecy by the SEELE-appointed Human Instrumentality Committee, attempts to control the Third Impact in an effort to induce the artificial evolution of mankind, because according to the Dead Sea Scrolls humanity has reached its evolutionary potential.
Very few details about the Human Instrumentality Project are offered, leaving it among the show's greatest mysteries. However fundamentally the effort involves the merging of the Fruit of Knowledge (Lilith-based life) with the Fruit of Life (Adam-based life), and to this end fans have observed three distinct methods by which the project can reach completion:
The ultimate goal of the project is to break down the walls that separate humanity into individuals—the AT Fields. According to SEELE, this will supplement and evolve humanity into a single-form organism where all Souls are one, and are therefore content. This unified state is believed to be a nirvana without rejection, loneliness, pain, or suffering, where one's weaknesses are complemented by another's strengths. The project is therefore the New Genesis that the series revolves around, an effort to evolve humanity into a singular consciousness via the use of the Sephiroth System (see Tree of Life). While some perceive this as elevating humanity into a being equal to God, others see it as the indiscriminate death or genocide of mankind.
NERV Commander Gendo Ikari has his own plans for the Human Instrumentality Project. The reason for his continuing involvement is to be reunited with his late wife Yui Ikari, which he believes he can accomplish by controlling the Instrumentality process. He intends to do this by implanting Lilith's Soul into an easily influenced vessel (Rei Ayanami), and eventually merging it with Lilith and Adam.
This leads to conflict between NERV and SEELE, resulting in the destruction of New Tokyo-3 and NERV Headquarters at the hands of the Strategic Self Defense Force. While Gendo successfully merges Lilith and Adam, ultimately Rei Ayanami rejects him, instead giving control of the Instrumentality process to his son, Shinji Ikari. In the end the Human Instrumentality Project follows neither Gendo's nor SEELE's scenario, as seen in The End of Evangelion.
Based on Neon Genesis Evangelion Platinum: 05 DVD Booklet