Following the events of "Harukanaru Toki no Naka de 2," which took place two centuries after the original anime's timeline, a substantial period has passed in the past, while only a short time has gone by in the future. High school student Kasuga Nozomi meets a mysterious young man on her school grounds, and he transports her through time and space to Kyou, a realm resembling Kyoto near the end of the Heian era. There, the Minamoto (Genji) clan, led by Minamoto no Yoritomo, is in conflict with the Taira (Heike) clan, commanded by Taira no Kiyomori. The Heike aim to overpower the Genji by unleashing malevolent spirits that disrupt the natural energy of the land and spread terror among the people. It is later revealed that the boy is actually Hakuryuu, the human form of the White Dragon God who protects Kyou, though his power has been weakened by these evil spirits. As the Hakuryuu no Miko (the Priestess of the White Dragon God), Nozomi sides with the Genji, understanding that Hakuryuu must recover his strength before she can return to her own era.