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 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.

Adashino-sensei is looking to buy some of the items that Ginko has obtained on his journey. He especially wants the wine cup that was drawn by Shinra, But Ginko says it's too rare to be sold to collectors. He tells Adoshenei-sensei about the strange being he met while in the forest and he also explains how the swamp is moving towards the sea. This looks like the work of a Mushi...

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.

"When all are sheltering within, there comes an imitation of spring. Linger in bliss for too long and your flesh will soon be frozen..."

Caught in a blizzard, Ginko is decides to look for shelter and finds a home where the owner, Suzu allows him to stay the night. The next day Ginko sees a boy, Miharu who seems to be fascinated by Mushi. Ginko learns that Miharu once disappeared into the mountains in the winter and then suddenly came back in spring, able to see Mushi. Miharu has been repeating this since and it may be caused by a "Harumagari" so in the end, Ginko decides to teach him more about Mushi.

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.