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.
The red dummy plugs we see injected into the Mass Production Eva series before they launch are labeled "Kaworu".
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.