

Shinji initially makes the wrong choice, to end all humanity and initiate Instrumentality.

Rei III shuts down his plans and gives this power to Shinji instead. Gendo correctly believes that he can manipulate Instrumentality and see Yui again if he can become "God" and merge with Unit 01. SEELE believes Instrumentality is the next step in evolution, but logically speaking, it's just a return to the nothingness before creation, bodiless souls and a primordial soup.

He has the choice of accepting or rejecting Human Instrumentality. Shinji, for one brief moment, essentially becomes God.
