In creating this adaptation, the intent was to mainly adapt “Birth”, “Assassins”, “The Mythos Cyborgs” and “Underground Empire of Yomi”, and have the four arcs make up the main composition of the series while adding a contemporary spin to the storyline. Yomi would also mark the end of the series, as Ishinomori had first intended.
To spread out the time between these four arcs and develop the characters further, newly-created stories were devised, along with loosely sourcing from stories in the Adventure King, Shojo Comic, and Weekly Shonen Sunday runs of the manga. The “Vietnam” arc would be re-purposed for a two-part mini-arc involving the fictional country of Muamba (along with providing a revised backstory for Cyborg 008), while the side-stories “A Phantom Dog” and “The Aurora Strategy” were also picked to be adapted.
As a way of keeping historical references in some backstories and as a way of creating a generation gap in the team, the creative team also introduced the concept of the “First Generation Cyborgs” and “Second Generation Cyborgs”: 001-004 had actually been abducted and remodeled in the early 1960s, but were frozen for 40 years due to the technology not being up to par with what Black Ghost wanted. Some team members also underwent significant change to their personality as well (seen most significantly with Cyborgs 002 and 004).
With the collaboration of Kawagoe as director, as well as the series configuration writer Shinsuke Onishi and character designer Naoyuki Konno, various new guest characters were also devised for the series, drawing inspiration from other manga works by Shotaro Ishinomori. Other characters from the manga also underwent alteration, and the “Mutant Warriors” arc (episodes 39-42) was an anime-original creation loosely paying homage to some elements and characters from the “Immigration” and “People Drifting Between Space and Time” stories from the manga.