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 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.

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.

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.

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Also 11th canon episode of the second season. At the request of Tanyuu Karibusa, Ginko sets off to investigate a phenomenon that might be related to a dangerous mushi, much to the chagrin of Kumado Minai, the current head of a long line of mushishi, who’s in charge of the area. As Ginko and Kumado get to the bottom of the Path of Thorns, the secret of the Minai line of mushishi is revealed.