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.

Misato brings Shinji, along with Touji and Kensuke, to a massive UN naval convoy transporting Evangelion Unit-02 and its fiery German pilot, Asuka Langley Souryuu, to Japan. Escorting Asuka is Misato's old boyfriend, Ryouji Kaji. After some awkward introductions and reunions, the fleet is attacked by a massive aquatic Angel. Asuka powers up Eva-02, and decides that she will defeat the Angel by playing "hopscotch"...