100 years have elapsed since the conclusion of Harukanaru Toki no Naka de 2, a time period that amounts to very little in the grander scheme of things. One day, Kasuga Nozomi comes across a strange boy at her high school who transports her through time and space to Kyou, a parallel world very similar to Kyoto during the Heian era's end. The Minamoto clan ("Genji"), led by Minamoto no Yoritomo, and the Taira clan ("Heike"), led by Taira no Kiyomori, are in conflict in this realm. The Heike seeks to vanquish the Genji by unleashing vengeful spirits to disrupt the land's natural energy flow and unleash terror in the region. The boy is the human embodiment of Hakuryuu, the White Dragon God protecting Kyou, who is now weakened by the presence of these restless spirits. Nozomi takes on the role of Hakuryuu no Miko (The Priestess of the White Dragon God) and forms an alliance with the Genji. Until Hakuryuu regains his strength, she's unable to return home, rendering her allegiance to the Genji essential.