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.

Ginko is on another adventure as he is brought to a very peculiar island, by a young boy Nagi. Ginko is taken to see a girl, who the island inhabitants refer to as "Ikigami" and is said to be able to perform miracles however Ginko discovers that there is more to this.

"Don't let yourself be blinded by fear and anger. Everything is only as it is..."

A boy named Yoki, who's able to see Mushi, was found in the woods by some mysterious lady named Nui with only one eye. It turns out that Yoki was travelling with his mother when a mudslide crushed his mother and he was left all on his own. Yoki's leg later heals itself however he doesn't seem to have anywhere to go so he stays with the Nui and begins to learn some things about the Mushi known as "Tokoyami".

"When all are sheltering within, there comes an imitation of spring. Linger in bliss for too long and your flesh will soon be frozen..."

Caught in a blizzard, Ginko is decides to look for shelter and finds a home where the owner, Suzu allows him to stay the night. The next day Ginko sees a boy, Miharu who seems to be fascinated by Mushi. Ginko learns that Miharu once disappeared into the mountains in the winter and then suddenly came back in spring, able to see Mushi. Miharu has been repeating this since and it may be caused by a "Harumagari" so in the end, Ginko decides to teach him more about Mushi.

Ginko arrives at a secluded place, to meet an old acquaintance, who seems to be in charge of a large volume of archival, confidential text. Ginko is allowed to read it, and discovers it is the work of Tan'yu, a writer. Tan'yu is the descendant of the Karibusa family, being born with a black mark on a part of their body.

"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.

"All that is in my world... is seem sound taste and touch. That is all. That is enough..."

Finally able to reach a city, Ginko comes across a "biwa hoshi" named Amane, singing songs about Mushi and she is immediately able tell that he is a Mushi-shi. So she forces him to stay a night at an inn when she later reveals that she once saw a "Ganpuku" a very rare Mushi that will make the host see better and better until they die.

Taku is a peculiar young boy who has always wondered who the people were that always passed by the mountains during the rainy seasons. One day he meets a boy named Isaza, while catching fish. It seems that not only Taku can see the Komiyaku in the mountains however Isaza seems to know a lot more about the mountain than him.

"The world is filled with life unknown to man..."

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.