Contains spoilers for this episode and earlier episodes.
Fuyutsuki disappears, and Nerv takes Misato into custody because her relationship with Kaji makes her part of the investigation. Seele is holding Fuyutsuki and questions him about Gendo's intentions, prompting memories of the years before Nerv. He recalls meeting Yui as a promising student and initially disliking the man she chose to marry. After Second Impact, his investigation challenges the official explanation of the catastrophe. Gendo introduces him to the underground laboratory and its work on the Evangelions. Other memories follow Ritsuko's friendship with Misato and Kaji, while Yui's disappearance during an experiment leaves Gendo determined to pursue the Human Instrumentality Project.
The account also reveals Naoko Akagi's work on the Magi and her relationship with Gendo. When a young Rei repeats cruel remarks she has heard him make about Naoko, the scientist kills the child in a jealous rage. Horrified by her action, Naoko then dies, and Gehirn is reorganized as Nerv. In the present, Kaji releases Fuyutsuki even though helping him places his own life at risk. Misato is freed after the missing commander is recovered. Kaji later greets an unseen person before a gunshot ends the meeting. At home, Misato listens to his recorded farewell and breaks down. Shinji hears her grief but cannot bring himself to comfort her.