The protagonist, Shinji Ikari, is a 14-year-old boy who is summoned by his estranged father, Gendo Ikari, the head of NERV, to pilot Evangelion Unit-01. Though reluctant, Shinji agrees to take on the responsibility of piloting the Eva to protect humanity. Alongside him are fellow pilots Rei Ayanami, a mysterious and emotionally distant girl, and Asuka Langley Soryu, a brash and confident pilot. Together, they fight the Angels under the guidance of NERV's staff, including the operations director Misato Katsuragi.

As the series progresses, it delves deeper into the characters' psychological struggles, particularly Shinji's relationship with his father and his battle with depression, self-worth, and identity. The trauma and emotional strain of piloting the Evangelions take a heavy toll on the characters, highlighting the cost of their fight for survival. Alongside the personal conflicts, there are numerous revelations about the true nature of the Evas, the Angels, and NERV's ultimate goals, including the secretive Human Instrumentality Project, which seeks to forcibly evolve humanity.

Neon Genesis Evangelion is renowned for its complex narrative, thought-provoking symbolism, and dark, introspective themes. It blends traditional mecha action with deep psychological and existential questions about the human condition, making it a defining and influential work in the world of anime.