As the Evangelion fandom wiki says, she died in 2004 as a result of her Contact Experiment with Unit-01, but her spirit lives on within the Eva as eternal proof of humanity's existence. Other than that, we can only deduce more from the discussion between Yui and Prof. Fuyutsuki from when Shinji was very small.
I don't want to contradict what we are told happened, I just want to add some elements that might explain some things.
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My perception of Neon Genesis Evangelion
Science FictionThis is what I believe about some parts of the popular anime Neon Genesis Evangelion. I will talk about both the main series and the movie "The End of Evangelion". Please don't forget that this is just my opinion, and I might contradict some canon f...