Misato is upset with Shinji for ignoring her orders in the last Angel battle, and he is so overcome by the stress of being an EVA pilot that he runs away. After wandering around Tokyo-3 for several days, Shinji is faced with the choice of quitting or staying in his new home.

It seems like it's an important day for nearly everyone at NERV. Misato and Ritsuko are going to a wedding; Shinji and Gendo are visiting Yui's grave; Asuka has a date. However, important things will spring from these seemingly mundane events.

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.