The first two-thirds of the series follow a semi-episodic format, introducing the world, the Angels (monstrous invaders), and the child pilots of the giant biological mecha known as Evangelions.

| Episode # | Title | New Content in Director’s Cut | | :--- | :--- | :--- | | | "Nerufu, Tanjō" (The Birth of NERV) | Extended flashbacks revealing the Second Impact, the murder of Dr. Naoko Akagi, and the true nature of Rei. | | 22 | "Semete, Ningen rashiku" (At Least, Be Human) | Extended mind-rape scene of Asuka by the Angel Arael; deeper exploration of Asuka’s childhood trauma with her mother. | | 23 | "Namida" (Tears) | Rei’s death and replacement; longer conversation between Ritsuko and Misato about the "Rei system" and dummy plugs. | | 24 | "Saigo no Shisha" (The Final Messenger) | Extended introduction of the final Angel, Tabris (Kaworu Nagisa); more dialogue about Lilith and Adam. |

For the 2003 Renewal and subsequent home video releases (including Netflix), episodes 21 through 24 were significantly extended with new footage (totaling over 30 minutes). These “Director’s Cuts” are considered the definitive versions, as they add crucial backstory and foreshadowing.

| Episode # | Title | Summary | | :--- | :--- | :--- | | | "Owaru Sekai" (A World That Is Ending) | "Do you love me?" A stream of consciousness where Shinji, Asuka, Rei, and Misato confront their inner selves in an abstract, white-space setting. | | 26 | "Sekai no Chūshin de Ai o Sakenda Mono" (The Beast That Shouted "I" at the Heart of the World) | The climax of Instrumentality. Shinji rejects merging into a single consciousness. The final scene features the cast congratulating him in a surreal, live-action-tinged sequence. |