Gendo Ikari's muted final words to Ritsuko were never scripted. There was originally meant to be an explosion in the background making the line inaudible, but even after it was cut Anno still wanted the line to be unheard. Yuriko Yamaguchi (voice of Ritsuko Akagi) had difficulty delivering the subsequent line "Liar" without knowing what Gendo had said. Anno gave her one small hint as to what the line was, and she instantly knew exactly how to delivery the line. To this day, only Anno and Yamaguchi know what that hint was.
Much like the story about Pink Floyd's "Dark Side of the Moon" to match with "The Wizard of Oz", this film is said to match with Nine Inch Nails "The Downwards Spiral". If played together, "Hurt" will coincide with Third Impact.
The film was based on the scripts Gainax originally intended to use for episode 25 of the TV series, but were unable to due to budget and production problems, and TV Tokyo's refusal to allow the episode to be produced for television broadcast. The second half of the film builds upon the script to create an ending concurrent to the one shown in the TV series.
According to Misato, the computer screen she is viewing near the beginning of the film is a file which reveals the truth of Second Impact. In reality (from what is legible) it is nothing but a short bio on Gainax and its films.
Asuka's voice actress, Yuko Miyamura, mentioned in an interview that Asuka's final line in the movie was her own idea. The original script called for the line "An'ta nanka ni korosareru no wa mappira yo!" ("I'd hate to be killed by a bastard like you!"), but Miyamura, Megumi Ogata (the voice actress who played Shinji) and director Hideaki Anno were at a loss over how the line should have been delivered; Ogata even attempted to strangle Miyamura in frustration. Finally, Anno told Miyamura to imagine a stranger masturbating over her while she was sleeping; he also asked her what she would think or say upon waking and realizing what had happened. Miyamura's reply: "Kimochi warui" ("I feel disgusting").
An alternate sequence was originally planned for the live-action portion of the film. In it, Shinji dreams of a world that exists without him. The sequence follows live-action versions of Asuka, Misato, and Rei in various stages of their daily lives, without NERV, Angels, or Evangelions. It ends with Asuka being followed by an "invisible" Shinji, who realizes in monologue that this is not reality. As the transition from live-action back to animation is made, Rei and Shinji discuss the nature of dreams vs. reality, as seen in the final cut of the film. Portions of this alternate sequence can be seen in the original theatrical trailer, which is shown on the R1 DVD before the movie plays.
While recording the scene in which Shinji strangles Asuka, Ogata Megumi (Shinji) became so frustrated and agitated that she actually pushed Miyamura Yuko (Asuka) to the floor and strangled her. Because of this, Miyamura had difficulty speaking her lines for a while.
The title of the film's second half, "Magokoro wo Kimi ni" (Sincerely Yours), comes from the title of the Japanese version of Charly (1968), which was based on Daniel Keyes's "Flowers For Algernon". "Magokoro wo Kimi ni" was reportedly the title given to the first edition of Keyes's story when it was released in Japan.