Shinji is immediately hit by one of Ramiel's attacks and is forced into retreat by Misato. With Rei still unable to enter battle, Ramiel approaches, and Gendo sorties Unit-01 with Shinji as the pilot. A bit shaken up, Shinji follows Rei to NERV, returns her ID card, and asks her about his father when he tells her that he has no faith in Gendo, she slaps him. Soon thereafter, Ritsuko has Shinji return Rei's ID card to her Shinji accidentally walks in on Rei as she is getting dressed, and clumsily knocks her to the floor, touching her naked body. Shinji begins to eye Rei, though he brushes it off as a curiosity about why she is always alone. After asking Ritsuko about them, she describes an incident where Gendo put his hands on scalding metal to save Rei, to which Shinji is skeptical. Later, at NERV HQ, Shinji sees Rei happily chatting with Gendo, who has burns on his hands. After being reprimanded by Misato, Shinji overcomes his own weakness and stays with NERV, and goes back to live with Misato. The next day, agents from NERV come and take Shinji back to NERV HQ. Because of this, Shinji spends several days wandering the town, until he sees Kensuke and spends the night with him. However, before defeating the Angel, Shinji's battle puts two of his classmates in serious danger. Shortly thereafter, Shamshel attacks, and Shinji pilots Unit-01 once again.

When it is discovered that Shinji is the pilot of Eva Unit-01, Tōji beats him up, in retaliation for his little sister being injured in the Angel battle. Several weeks later, Shinji begins to attend school, where he meets Tōji, Kensuke, and Hikari.

Shortly after the Angel's defeat, Misato Katsuragi takes Shinji to live with her rather than letting him live on his own. Reluctantly, Shinji agrees to pilot the unit, and is able to defeat Sachiel after his Eva goes Berserk. After refusing to do so, Gendo brings in a backup pilot, Rei Ayanami, who is so badly injured that she falls while trying to get off a stretcher. Shinji first appears in Episode 1 at age fourteen, where he has been summoned to Tokyo-3 by his father, Gendo Ikari, to pilot Evangelion Unit-01. As he witnessed this event, he was subjected to considerable trauma that had lingering effects upon him.

Around the age of three, Shinji lost his mother to the Unit-01 Contact Experiment.

Evangelion shinji ikari voice actor