Misato has been promoted to Major, but the celebration does not last long. A monstrous Angel appears in Earth orbit right when Gendo and Fuyutsuki are away, leaving her and the children to deal with a colossal kamikaze threatening to drop itself right on top of Tokyo-3.

Kouzou Fuyutsuki is kidnapped and interrogated by Seele, who are horrified over the results of the last encounter with an Angel. He recounts his past, providing flashbacks into the creation of Nerv. The pasts of Misato Katsuragi, Ritsuko Akagi, Rei Ayanami and Yui Ikari are also revealed. Ryouji Kaji, meanwhile, decides to find out the truth, no matter the cost.