Shinji Ikari yearns for excitement to transform his boring day-to-day life as a student at the NERV Foundation Academy. His wish is granted when he witnesses an explosive battle between two teenagers and an older man with great wings extending from his back. Shinji recognizes these two teenagers as his classmates: his crush Rei Ayanami and new transfer student Kaworu Nagisa.

During the encounter, Shinji unwittingly releases a power that appears to vanquish the winged man; in future instances, his power takes the form of a gun-like EVA, a weapon manifested from his will to survive. He learns that the beings his classmates combat are known as Angels, transient forms of consciousness that take possession of human bodies because they lack physical forms of their own. Cooperating with his two classmates—and later joined by foreign transfer student Asuka Langley Souryuu—Shinji agrees to fight against the Angels who plague his town.