Director Hideaki Anno fell into a deep depression following completion of work on Nadia: The Secret of Blue Water and the 1992 failure of the Royal Space Force: The Wings of Honnêamise sequel project. According to Yasuhiro Takeda, Anno agreed to a collaboration between King Records and Gainax while drinking with King representative Toshimichi Ōtsuki; King Records guaranteed Anno a time slot for "something, anything". Anno began development of the new series in 1993 around the notion of not running away, which had been the underlying theme of Aoki Uru, an earlier Anno project that had failed to move into production. Early into the production, Anno stated his intent to have Evangelion increase the number of otaku (anime fans) by attracting interest in the medium. According to him, the plot of the series reflects his four-year depression. In the early design phase of the Evangelion project several formats were considered, including a film, a television series and an original video animation (OVA) series. The producers finally opted for the television series as it was the most widely accessible media in Japan at that time. The proposed title Alcion was rejected due to its lack of hard consonant sounds.
Evangelion borrowed certain scenarios and the use of introspection as a narrative device from a previous Anno project entitled Gunbuster. He incorporated the narrative structure of Nadia and multiple frames of reference to leave the story open to interpretation. Over the course of the writing process, elements of the Evangelion storyline evolved from the original concept. A female protagonist was initially proposed for the series, but the idea was scrapped. Originally, the first episode presented the battle between an Angel and Rei, while the character of Shinji was only introduced after the Angel had been defeated. Further changes to the plot were made following the Aum Shinrikyo sect's sarin gas attack on the Tokyo subway in March. Azuma Hiroki has said that the original Evangelion story was "too close to reality" from Anno's point of view. Basically, Anno thought that the original scenario was not suitable for broadcasting, and he feared censorship. However, he also criticized Aum Shinrikyo, because "they lost any contact with reality". For this reason, Azuma stated that Evangelion "is an intrinsic critique of Aum".
The final version of the story reflects inspiration drawn from numerous other anime and fictional works. Chief among these are Space Battleship Yamato, Mobile Suit Gundam, Devilman and Space Runaway Ideon. The series also incorporates tributes to Childhood's End, the novels of Ryū Murakami, The Andromeda Strain, The Divine Invasion, the poem Pippa Passes, The Hitcher, and several television series including The Prisoner, Thunderbirds, Ultraman and Ultra Seven.
The development of the Neon Genesis Evangelion series ran close to deadlines throughout its production run. The initial cuts of the first two episodes were screened at the second Gainax festival in July 1995, only three months before they were aired on television. By episode 13 the series began to deviate significantly from the original story, and the initial script was abandoned. The number of Angels was reduced to 17 instead of the original 28, and the writers changed the story's ending, which had originally described the failure of the Human Instrumentality Project after an Angel attack from the moon. Starting with episode 16, the show changed drastically, discarding the grand narrative concerning salvation for a narrative focusing on the individual characters. This change coincided with Anno's development of an interest in psychology after a friend lent him a book on mental illness. This focus culminated in a psychoanalysis of the characters in the two final episodes. The production ran so close to the airing deadline that the completed scenes used in the preview of the twenty-fifth episode had to be redesigned to work with the new ending. These episodes feature heavy use of abstract animation, flashbacks, simple line drawings, photographs and fixed image scenes with voice-over dialogue. Some critics speculated that these unconventional animation choices resulted from budget cuts, but Toshio Okada stated that Anno "couldn't decide the ending until the time came, that's his style". These two episodes sparked controversy and condemnation among fans and critics of the series, including significant vitriol directed at Anno himself. Hideaki Anno and Studio Gainax released in 1997, two animated feature films: Death & Rebirth and The End of Evangelion.