During Third Impact, Human Instrumentality, the merger of all of humanity into a single life form, is nearly achieved. However, Instrumentality is eventually rejected and reversed under the direction of Shinji Ikari.

Does Shinji accept instrumentality in End of Evangelion?

Acceptance of Instrumentality

Another theory is in EoTV Shinji accepts Instrumentality while in EoE Shinji rejects it. In EoTV it does not make it clear that Shinji has a choice in the matter; he just needs to accept it after he realizes to love himself.

What does Shinji realize at the end?

Shinji realizes that he created an isolated, empty world for himself where no one can hurt him anymore. Episode 26 begins, and Instrumentality rockets toward its conclusion.