Deputy Commander Kozo Fuyutsuki is kidnapped and interrogated by Seele, who are outraged that in its last battle Unit 01 absorbed the S² engine from an Angel into its body, so that it no longer requires an external power source and can now function indefinitely. Meanwhile, Kaji goes AWOL to try to find out the truth about NERV. As Fuyutsuki is interrogated by Seele, he recounts in flashbacks how he first met Gendo and Yui, the dark events surrounding Second Impact, and how NERV and the Evangelion project were born. Flashbacks also reveal the history of Misato, Ritsuko, and Rei. Fuyutsuki is rescued by Kaji, and Fuyutsuki warns him that Seele will want him dead now. That evening, Kaji is shot by an unseen assassin. Misato receives a voicemail from Kaji, in which he urges her to continue his search for the truth about NERV, and from its nature she deduces that he is dead and breaks down in grief.