Genesis Rainbow's tells the story of a mysterious entity named FLY, a nameless, bodiless, and willless abstract being created by Ontarios, the God of Creation, in a cosmic realm known as Sonata Expellion. Created from data, information, and a newly formed consciousness, FLY is tasked with finding Aoi Hiroshi, a figure who has been missing since a great battle in the past. However, to interact with the outside world, FLY needs a host.
After being thrown out of the cosmic current, FLY eventually falls to Earth in the form of a strange phenomenon resembling a comet.
In a dark forest, a teenager named Rei unwittingly becomes both a witness and a victim of this event. As Rei attempts to approach the alien entity, mysterious shockwaves and time distortions begin to occur, indicating that their encounter is no ordinary occurrence.