The film takes place one year after the events of the anime series. After going through a painstaking journey across multiple World Lines due to the invention of D-Mail, text messages that can be sent to the past, Okabe Rintarou has assumedly landed in the Steins Gate World Line, in which none of his friends would have to die and a future ruled by SERN due to the invention of a time machine no longer exists. However, Rintarou soon starts feeling the side effects of his constant time travelling across multiple World Lines, which soon builds up and causes Rintarou to suddenly vanish from existence, with only Makise Kurisu, the girl who he had saved thanks to his efforts, remembering him through déjà vu. It is now up to Kurisu to find a way to get Rintarou back.

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