At the end Shinji and Asuka sailed for Aman
The ending is remarkably similar to the ending of The Lord of the Rings
, in which Frodo's scars were too severe and he could not fit in The Shire anymore so he said goodbye to their friends and sailed towards Aman, leaving Middle-Earth forever.
The narration says that Shinji and Asuka left human civilization forever. Human
civilization. Clearly, as a reward of Eru
by defeating the Great Old Ones, Gandalf or another emissary of the Valar
offered Shinji and Asuka the possibility of sailing to Aman where they could heal and live happily together forever.
At some point of the crossover they will travel to the original and Rebuild universes. Butts will get much ass-kicking, Gendo
and even Yui
will get a reckoning, each Canon Shinji will get his red-haired girl
and each Canon Asuka will get her not-so-wimpy-now Shinji