Shinji begins attending his new school in Tokyo-3, and has a difficult time dealing with the fame of being an Evangelion pilot. Touji Suzuhara, who's little sister was injured in Shinji's fight against the Angel, is angry at Shinji. A new Angel appears, and Shinji must once again pilot EVA-01 to defeat it.

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.

EVA-00 is finally repaired, and Shinji tries to get to know its enigmatic pilot, Rei Ayanami, better. However, he is confounded because she is extremely insular, has no friends at all, and the entire record of her past has been erased. In the midst of this, a very powerful Angel, the floating monolith Ramiel, attacks Tokyo-3.

The EVA pilots are disappointed to find out that they are not allowed to go on their class trip to Okinawa, because they have to stay at Tokyo-3 to stay on-call in case of an Angel attack. Meanwhile, a new Angel is discovered in a chrysalis-like developmental stage deep within the magma of the volcano Mount Asama.

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.

A routine test involving the EVA pilots turns into a struggle for survival when a wholly new type of Angel appears and spreads inside NERV HQ. This new, computer-like angel threatens to set off the self-destruct for the entire facility, leaving Dr. Ritsuko Akagi in a race against time to save the GeoFront and destroy the Angel.

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.

Enraged over Touji's near-death at the hands of his own EVA, Shinji refuses to pilot an Evangelion again and prepares to leave Tokyo-3 for good. He is forced to reconsider that decision when an immensely destructive new Angel attacks just as he is about to leave...

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.

Too frightened to face Misato or Rei, Shinji runs away yet again, only to meet and strike a friendship with Kaworu Nagisa, the replacement pilot for EVA-02. Kaworu's openness and friendliness provide much-needed comfort for the disturbed Shinji. However, suspicions abound over Kaworu's incredible synchronization abilities.