The villains, (SEELE) a secret organization who secretly control world governments, want to fuse all humans in to one to bring back their satanic god.
Now look at whats happening. They want to fuse men and women with transgenderism and nonbinary shit, they want to fuse countries and remove borders and create a one world government and they want to fuse races with race mixing.
Shin Godzilla is really good, and my friends (who are Godzilla dorks, but not Eva dorks) thought it was very accessible, and may not have gotten the subtext about it being about the Japanese government's response to the 2011 earthquake/tsunami/nuclear meltdown, but neither did I, honestly, until I read it. Check it out! Great movie.