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 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.
Kozue loves to stargaze and does so regularly. On a trip to view a meteorite, she happens to meet a boy named Ginga. He has a mysterious ability to discover more information about the stars, which he uses to help scientists with astronomical research. Unfortunately, his life is mostly dictated for him, and when carrying out missions, he must always wear a protective suit. Kozue helps Ginga to gradually take control of his life by encouraging him to make his own decisions.
Ginko, a Mushi master, travels from place to place researching the Mushi and helping people who are suffering because of it.
