Karin Hanazono is ready to settle down and live life without her heavenly powers until she is told in a dream to search for the "Three Honored Gods." When she awakens the next morning, she is shocked to find a small child sleeping peacefully in her bed. Introducing himself as her future son, Suzune tells Karin about the dire fate that awaits her and his father unless she can destroy the "Seeds of Chaos." In order to do so, she must assemble three gods—Uranus, Hades, and Neptune—and combine their powers to eliminate the threat.

Having already identified Kazune Kuujou as Uranus, Karin must also find Hades and Neptune in order to save Suzune's future from ruin. At the same time that she sets out on her journey, a mysterious and sinister girl appears, sowing Seeds of Chaos wherever she goes. Now, with the power to travel through time, Karin must do everything she can to find the remaining two gods and the origins of the Seeds of Chaos before it is too late.