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!

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.

On a rainy day Ginko takes a rest from his travels and comes across a man named Kourou who seems to be obsessed with a rainbow. To pass the time Kourou reminisces in his past, with the events which led to him pursuing rainbows whenever they appear. Ginko explains to him that the rainbow which he is searching for is actually a Mushi known as "Koda" but there seems to be more to it.

Ginko arrives at a village where the men are in a heated discussion about the mountain. After learning of Ginko's identity they ask for his help to find another Mushi-shi called Mujika, who happens to be the master of the mountain. While on his trek through the mountain Ginko stumbles across a boy who's also looking for Mujika. Later they manage to find Mujika but this isn't the end of it.

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".

In a cold mountainous region, Ginko is wandering around the snow cover plain when he hears a sound ringing through the cold air and he also notices some rust on a tree. Ginko enters a nearby town to find the rust covering everywhere, including the people. The village chief tells Ginko that this is a sickness that has been affecting the town for 14 years that the people have been slowly losing the movements of the limbs and it's said that a girl called Shige is the cause of it.

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..."

Історія про затемнення сонця та зміни, які трапляються під час нього: поява колони муші, зміна поведінки тих, хто боїться світла, порушення сну, зникнення людей. На щастя, мушіші підготовлені до всього, однак Ґінко доводиться стикнутися ще з одним клопотом — муші Хіхамі, який харчується сонячним світлом.

A restless man, Kanta, on his way home to his wife and young daughter (Futaba), sits down to rest in a forest. He is tired and thirsty so he eats a red fruit that was lying on the ground near him, and gives thanks to the plum. Some time after this, he starts having vivid memories both in his dreams and while awake of times going back before his birth. He goes looking for a huge tree but finding it does not make him happy.