The manga was illustrated and written by Takeaki Momose. Momose was one of the candidates for character designer on the series, but Izubuchi wanted Akihiro Yamada to do the original designs, and Hiroki Kanno got the job of adapting them for animation. With the manga Momose got the opportunity to re-design the characters into his own style and make changes in characterization and story, as well as adding “fan service”.
The scenario of the manga adaptation is similar to RahXephon series with some minor and major differences. In the anime series, Reika is a mysterious and distant figure; in the manga Reika is a more comical figure who grew up as Ayato’s adoptive sister with a darker origin. The anime series shows Megumi competing with Haruka for Ayato’s affections, while this role is taken by Reika in the manga. The rate of time dilation is also different in the manga version, as the year outside Tokyo is 2033 instead of 2027.
The manga release started before the anime broadcast, so that the ending in one medium would not trail too far behind the other. The first chapter, or “mission”, appeared in the magazine Monthly Sunday Gene-X in the October 2001 issu (released 19 September 2001); the final chapter was released two months after the airing of the last anime episode, in the December 2002 issue (released 19 November 2002).
The chapters were subsequently released in three compilation volumes which were translated and published internationally. These volumes contain the following chapters and extras. In addition, each publisher may have added certain notes and advertisements in the front and back of the volumes.