Enjoying a peaceful life in New-Tokyo 3, high school student Shinji Ikari spends the days with his close-knit group of friends, consisting of his pushy childhood friend Asuka Langley Souryuu; slackers Toji Suzuhara and Kensuke Aida; student president Hikari Horaki; and the eloquent oddity Kaworu Nagisa. However, the arrival of bubbly transfer student Rei Ayanami shakes up the group's status quo, causing a web of love triangles, crushes, and confessions to come bursting forth. Yet the complex state of their relationships becomes the least of their worries when United Nations agency Nerv recruits them for experiments shrouded in mystery. As Nerv continues to impede on the students' lives, Shinji and his friends are set on an irreversible path, with their angelic days long behind them.

An alternate retelling of a classic anime series, Shinseiki Evangelion: Koutetsu no Girlfriend 2nd reinvents these characters as normal students in a world vastly different from the one presented in Neon Genesis Evangelion.