Kamiyama produced the film with the intent of doing a follow-up in the form of either a TV series or second film set in the same continuity, however, these did not come to pass. The character designs underwent revision for the new century, as well as to make them more realistic. Oshii stepped down from the full film project, leaving Kamiyama to take over as the director, and to also throw out Oshii's initial setting of 003 being 58 years old in the year 2013.

002 was also depicted as alive in the finalized concept film, although the fates of the others were not mentioned. Īfter Kamiyama had joined the project as screenwriter, the above setting was thrown out and tweaked to 009 living as a high school student with amnesia, while 003 would have to re-awaken his memories. Kenji Kamiyama had related this story as an anecdote in the book 'Anime Style 002' in 2012, after the release of the film. Oshii's plot was to also take cues from an unproduced 1985 Lupin III film he had planned out, where a giant 'Tower of Babel' would be present in Tokyo, which would house the fossil of an angel. 001 was said to be in the form of a dog, rather than a baby, and 003 had aged to her fifties while 009 remained physically in his teens.

In Oshii's first vision of RE: (prior to the demo film), all the 00 cyborgs except 009, 003, and 001 had passed away in the ensuing years, and 009 was holed up in an apartment in retirement while 003 and 001 had taken to traveling the world. Originally, Mamoru Oshii was assigned to the project in 2009, and would later create a short CGI demo film that was screened in September 2010, titled 'Cyborg 009: The REopening'. In re-imagining Cyborg 009 for the year 2012, 'RE:' was included in the title, indicating the movie as a sequel to the original manga (taking place 27 years after Ishinomori's last arc in 1986) as well as symbolizing a 'restart' for the franchise.

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