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.

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".

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".

"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.