A girl named Sui has an unusual disease that causes pain in her eyes whenever she sees light. She has to be locked in a pitch black shed that has no light in it. A boy named Biki helps Sui by removing bandages, giving her food, and just talking to her. Biki's mother is worried about him getting the illness, so she tells him not to stay as long as he normally would with Sui. One day while Biki is talking to her, she tells him why she has that illness: There are Mushi in her eyes. Biki continues to take care of her until one night when he is reading by a candle, a strange pain comes to his eyes.

While on his journey, Ginko stumbles upon a town which has yielded a great crop this year, thanks to their ancestors. However, it is said that someone must be sacrificed in exchange. Ginko finds this peculiar and decides to investigate further, by going to see the village "Saishu-sama" (chief mourner) who may have something to do with it.

While resting in a bamboo forest, Ginko is approached by an odd man named Kisuke, who tells Ginko that he has been lost in the forest for 3 years. Ginko seems to have also become lost, and decides to go off and figure something out about the forest. After managing to get out of the forest, Ginko figures out that it's the work of a "Magaridake".

"Give birth to me once more. I want to meet you once more. I want to see this beautiful ocean once more..."

Ginko arrives on an island asking about the so called "Rebirths" but to no luck. At night he later meets a peculiar lady who happens to be able to see a strange light in the sea and she ends up inviting him to her home. She later explains to him what "Rebirths" are; when a person is about to die they can be taken deep inside the Ryuugu, where they are reborn.

A powerful mushi appears during an eclipse, drawing other mushi to form a huge shadow that blocks the sun over a small village. Looking for clues about the mushi, Ginko meets a child who is afflicted by a strange disease that manifests itself when she is exposed to sunlight, and it does not take long for him to find out that both facts are related.

A sake brewer once lost his way home and chanced upon a strange ceremony. There, he tasted a sweet, glowing sake that he's never been able to forget. Years later, his son has followed in his footsteps and is trying to brew a sake to match his dad's. When he, too, encounters a late-night ceremony, he pretends to be part of it, meeting Ginko during the occasion.

Ginko meets a woman with a striking beauty that lacks all five senses and according to the man who takes care of her, is over 80 years old and has lived in his family for generations. While investigating the mushi responsible for it, Ginko discovers an even darker secret involving the two.

While on board a boat, Ginko meets a young man who has developed a connection to a flock of bird-type mushi able to create wind.

On his way to answer a summons, Ginko is trapped on a mountain that has been sealed by the mountain lord, and is experiencing an eternal winter because of some trapped snow-mushi. Why has the mountain lord sealed the mountain, and how will Ginko escape this eternal winter?