After Nagisa Kaworu Nagisa was wiped out, NERV 's work seems to have ended, and the staff of various departments are discussing their future whereabouts in a peaceful atmosphere. At this time, the headquarters of NERV was suddenly attacked by the Strategic Self-Defense Force (hereinafter referred to as Zhan Zi). It turned out that Zhan had received news that NERV was attempting to cause the "third catastrophe," so they flaunted the slogan "Protect All Mankind" and carried out a brutal massacre on NERV staff. After killing Kaworu Nagisa of Nagisa , Ikari Shinji couldn't cheer up anymore and was immersed in painful thinking all day long, unwilling to deal with the attack of Zhan Zi and the EVA mass production machine from the Human Completion Committee .
Nervous breakdown of Shikinami Asuka Rangurē lost the will to live, but when threatened by war since the instant of lives are at stake, she felt the presence of the mother's EVA machine, and saw the mother's smile in the cockpit. Shikinami Asuka Rangurē, who broke through the heart barrier, woke up and fought a desperate battle with Zhan Zi and the EVA mass production machine .
Ayanami Rei , who was created to meet Ikari Yui again , came to the side of the dogmatic red pool at the center of NERV at the time of an appointment with Ikari Gendou . Whether it's a container for Ikari Yui's soul or a prop of " Neon Genesis Evangelion ", her destiny will end here, but what is the choice of Rei who already feels the existence of her own soul? Under Zhanzi ’s attack, Katsushiro Mitsuto not only completed Kaji Ryouji’s unfinished investigation of the truth about the "Second Catastrophe" and "Neon Genesis Evangelion", but also protected Shinji and Shikinami Asuka Rangurē and guarded against Seele ’s EVANGELION- 01 physical contact with the second unit, she was busy until she was hit by a stray bullet from Zhanzi.
Out of hatred for Ikari Gendou, Akagi Ritsuko accepted Seele 's proposal to detonate MAGI , but MAGI , who has Naoko Akagi's way of thinking, chose Ikari Gendou and abandoned his daughter, rejecting the proposal of self-destruction. After that, Ritsuko was shot by Gentang.
According to the " Dead Sea Scrolls ", the third catastrophe will surely be caused in more than ten years. Seele needs all the EVA to complete "Neon Genesis Evangelion". On the one hand, they informed Zhanzi NERV that they attempted to cause the third catastrophe, provoked Zhanzi to attack NERV, and on the other hand commanded the mass-produced aircraft to fight the EVA. Seele uses such a cruel method, and its purpose is to change the way of human material existence through rituals.
Ikari Gendou, Kozo Fuyuki, and Ikari Yui, who have worked with Seele for a long time , have brewed their own "Neon Genesis Evangelion" in order to prevent the "final tragedy" of mankind and guide mankind into the "new world". Ikari Yui disappeared during the experiment as a "subject" in 2004. Ten years later, Gendo and Fuyuki hope to complement the humanity through the fusion of Rei and Lilith, but before that, Gendo hopes to be able to cooperate with Ikari Yui. Get together. "Neon Genesis Evangelion" is implemented-Except for Shinji and Shikinami Asuka Rangurē, all human beings have lost their physical form and absolute realm and merged into a whole.