Ginko hears a rumor around town that a man is has prophetic dreams every once in a while. He suspects that Mushi are living in his dreams. He gives the man medicine to keep them under control and says he will come back when he has used about all of them. When Ginko returns, the village is deserted and torn up. Ginko finds the man alone in is house. The man then tells him about what happened while he was away.

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.

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.

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.

"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".

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".

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.

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 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.

Near a village by the sea, a girl lives with her father on a secluded crag. She wants to make friends, but her father, for some reason, doesn't want her associating with the village people. When Ginko arrives, he finds a mushi that's an omen of disaster. Will the girl's father be able to forgive past events and help the village?

While on board a boat, Ginko meets a young man who has developed a connection to a flock of bird-type mushi able to create wind.

On his way to answer a summons, Ginko is trapped on a mountain that has been sealed by the mountain lord, and is experiencing an eternal winter because of some trapped snow-mushi. Why has the mountain lord sealed the mountain, and how will Ginko escape this eternal winter?

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.

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.