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!

Some kids enter Adashino-sensei's shed and find a lot of strange things, but there's one thing in particular that interests them. It's night and Adashino-sensei is called upon to look at one of the kids, a girl who has become bitterly cold, and the cause is a mysterious ink stone she touched. Luckily for Adashino-sensei, Ginko is passing through the village, and he shows him the ink stone, which he identifies it as a "Kumohami".

It is spring, and Ginko is taking a boat through a river, when the boat's boy, Kaji, asks Ginko whether he could help his mother, who's forgetting things and can't sleep. At first glance it may appear to be progressive amnesia, however something isn't right.

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.

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.

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.

"Build a fire - night comes... Light a fire - darkness comes... Hide the fire - flames arisen from corpses creep in..."

Ginko meets another Mushi-shi, which happens to be a young lady called Yahagi and surrounding the village she lives in is a new variety of Mushi growing on the mountain's fields. It's becoming so bad that the village people are at risk and as a last resort they plan to burn the entire mountain but Ginko doesn't think that this is the right option.

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..."