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Theatre and literature
The areas of the Nerv headquarters, such as the Malebolge and the Cocytus, are named after portions of the Hell imagined in Dante's Inferno, while in the eighth episode, ships are presented with names from the works of William Shakespeare, such as the Othello, Cymbeline, Titus Andronicus and The Tempest. An official Death and Rebirth booklet described Rei Ayanami as "an expressionless Noh mask", while for writer Dani Cavallaro the choice faced by Shinji in The End of Evangelion is not a choice made by an individual character so much as "an allegorical, Noh-like emblem for humanity". Shinji has also been described as a tragic hero and likened to Oedipus. Writer and animation critic Patrick Drazen similarly compared the dilemma faced by Shinji in the twenty-fourth episode against the Angel Tabris to Hamlet, the protagonist of Shakespeare's tragedy of the same name.

According to Gualtiero Cannarsi, the editor who was in charge of the first Italian-language edition of the series, the Gainax studio members might have been inspired by James P. Hogan's Giants series, Arthur C. Clarke's short story "The Sentinel" and 2001: A Space Odyssey. The Apostolos would have been the servants and apostles of the giant Adam, the divine sentinel of a distant alien race formed long before humanity, drawing on Hogan's evolutionary and science fiction themes.

In a draft of the twenty-fourth episode of the series, which was shelved during production, Kaworu Nagisa's character would compare Gendo to Paul, the protagonist of Erich Wolfgang Korngold's opera Die tote Stadt, a character who locks himself in his home after the death of his wife, building a "Temple of the Past" with her belongings; and later  meets a young woman who looks similar to his late wife and falls in love with her. The Nerv base would be a "Temple of the Past" built by Gendo. Carl Gustav Horn, editor of the Neon Genesis Evangelion manga English edition, compared Kaworu as represented in the manga to the character Satan in Mark Twain's novella The Mysterious Stranger, for acting with indifference to human morality. Reviewer Toji Aida also likened Kaworu to a ghost of the Noh theatre who disrupt the events of the story in the tripartite Jo-ha-kyū structure of the Rebuild of Evangelion saga.

Alienation and loneliness
Accordng to Susan Napier, the alienation of the characters, especially that of Shinji, is particularly apparent in the final episode.

Anxiety and Japanese context
For Dani Cavallaro, the anxieties underlying Anno's work largely emanate from culturally specific vicissitudes affecting Japan in the early and mid-1990s, like the bursting of the economic "bubble", the Aum Shinrikyo terrorist attack and the Kobe earthquake. According to Cavallaro, the societies depicted in the Evangelion productions also capture a global notion of Sigmund Freud's "civilization and its disconcents".

Generational conflicts
According Dani Cavallaro, the generational conflicts in Evangelion do not only pertain tot he private sphere of the characters, since they simultaneously strike cultural chords, "insofar as Evangelion is also eager to document the generational connotations of Japan's social and economic modernization in the aftermath of the Second World War". For Dennis Redmond, the "old men" of Seele represent the conservative, immediate post-war generation; Gendo Ikari and Fuyutsuki "hail from the technocratic generation of the 1970s"; Misato and the other Nerv staffters represent the consumer-oriented 1980s, while the children themselves incarnate the informatic 1990s.