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.
You forgot the part when Yui achieves apotheosis by manipulating everyone including her husband and own son, and how she leaves everyone to die while everyone is distracted fighting the secret cabal
Wrong, she sacrificed her life to protect Shinji and become a mother to a new world