On a warm summer day, a boy heard the sound of bells ringing, as if in celebration, in the mountain near his home. Several years later in that same mountain, the mushishi Ginko stumbles upon a young girl in a mountain with branches and leaves growing out of her body. He later realises that she is the lord of that mountain but finds it strange that a human like her was chosen as the lord. He meets her older brother who has continued to search for her ever since she disappeared while accompanying him on a stormy day. The story is about Ginko’s peculiar journey amidst the occult to unravel the mystery behind the enigmatic girl called Kaya and the mountain that has become her home.

The film centers on Asuna, a young girl who spends her solitary days listening to the mysterious music emanating from the crystal radio she received from her late father as a memento. One day while walking home she is attacked by a fearsome monster and saved by a mysterious boy named Shun. However, Shun disappears and Asuna embarks on a journey of adventure to the land of Agartha with her teacher Mr. Morisaki to meet a Shun again. Through her journey she comes to know the cruelty and beauty of the world, as well as loss.

Fifteen girls who went on an expedition to an uninhabited island are left behind because their ship sank. The girls' survival begins.