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Yoshiyuki Sadamoto, the creator of the protagonist, Kite, stated that when creating Kite, he based his proportions on Naruto, a character from the popular anime series. At the time, he had no idea that CyberConnect 2 would eventually purchase the rights to the Naruto: Ultimate Ninja series.
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In the American releases, all four games received a "Mature Sexual Themes" content warning advisory because of an in-game article regarding internet pornography, even though Infection does not have this news cast. In Europe, Infection did not receive the "Mature Sexual Themes", whereas the other games afterward did.
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CyberConnect2 president and .hack series developer Hiroshi Matsuyama in an interview with IGN, said that the developers had researched some MMORPGs as inspiration for .hack, specifically mentioning Phantasy Star Online, Final Fantasy, and Ultima Online.