Shinra, a boy living in a forest with mysterious powers, calls for Ginko, The Mushishi, to help him with his problems. While Ginko is staying with Shinra, he tells him all about Mushi and his powers. Later on, while walking in Shinra's house at night, Ginko finds a Mushi... But this isn't an ordinary Mushi, it's Shinra's grandmother!

On silent snowy nights, when no sounds can be heard, many people go deaf in one or both ears. The doctors can't do anything, so they think it might be paranormal. Ginko looks into some of the villager's ears and he tells them that the cause is a Mushi called "Un". After dealing with their small problems there is one more person who has lost sound in both of his ears and his condition is very different than the other people's, as he has also grown four horns on his head.

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.

Just managing to cross the treacherous Kazura Bridge, Ginko meets up with a man on the other side who takes him to meet a lady called Hana, who fell from the same bridge 3 years ago. Even though Hana survived, all she does is sit under the sun and nothing else and nobody seems to know what's wrong with her. Hana is feared to be a "Tanimodori", which are people whose minds and memories are wiped clean and they die on the night that the "One Night Bridge" shows up. From the info gathered Ginko knows that Hana is possessed by a Mushi called a "Nisekazura".

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".

Seijirou is fascinated by the stars and enjoys stargazing. One day he was by the riverbed with the village nanny Fuki when she notices a string coming down the sky and as she tries to pull all of a sudden she disappears, right before Seijirou's eye. Ginko is travelling through the mountains and is being followed by a peculiar girl. It turns out that it's Fuki, who has been exposed to a strong Mushi presence and can't be seen by anyone.

A lady named Aki discovered a green stain on her wedding gown, one year later she gave birth to a boy who, now grown up, has the same marks on his body. It turns out that the boy was originally born not as a human but as some shapeless green blob, which then turned into a human. Her husband asks for Ginko's help yet he is unable to save her son because it's the work of a "Watahaki".

"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.

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..."