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?

Shigeru's daughter (Yuri) is found dead in the mountains. A painful skin infection breaks out in his village. Ginko can cure the disease of the villagers but Shigeru has a much more serious case. It turns out that he and the son of his deceased brother brought back the mushi causing the problem to the village when they broke a taboo.

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".

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!

On silent snowy nights, when no sounds can be heard, many people go deaf in one or both ears. The doctors can't do anything, so they think it might be paranormal. Ginko looks into some of the villager's ears and he tells them that the cause is a Mushi called "Un". After dealing with their small problems there is one more person who has lost sound in both of his ears and his condition is very different than the other people's, as he has also grown four horns on his head.

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.

"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.

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...

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."

This story is about a mysterious genius artist named Kai who left his family to become better known for his talents and as a parting gift his sister made him a Haori (Man's Kimono). One day he got bored and made a Haura (painting inside the jacket) on his Haori. His master saw this and recognized his talents, so he gave Kai jobs with clients and he quickly started to become well known for his work but his fame came at a price.

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.

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.

Ginko meets a woman with a striking beauty that lacks all five senses and according to the man who takes care of her, is over 80 years old and has lived in his family for generations. While investigating the mushi responsible for it, Ginko discovers an even darker secret involving the two.

Multiple lightning strikes have been observed hitting the same tree, and Ginko investigates. He meets a strange boy who attracts lightning to himself due to a mushi's influence. His mother believes he is doing it to spite her and struggles with the fact that she doesn't love her child.

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.

A girl named Sui has an unusual disease that causes pain in her eyes whenever she sees light. She has to be locked in a pitch black shed that has no light in it. A boy named Biki helps Sui by removing bandages, giving her food, and just talking to her. Biki's mother is worried about him getting the illness, so she tells him not to stay as long as he normally would with Sui. One day while Biki is talking to her, she tells him why she has that illness: There are Mushi in her eyes. Biki continues to take care of her until one night when he is reading by a candle, a strange pain comes to his eyes.

"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.

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.

"All that is in my world... is seem sound taste and touch. That is all. That is enough..." Finally able to reach a city, Ginko comes across a "biwa hoshi" named Amane, singing songs about Mushi and she is immediately able tell that he is a Mushi-shi. So she forces him to stay a night at an inn when she later reveals that she once saw a "Ganpuku" a very rare Mushi that will make the host see better and better until they die.

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?

Ginko visits a village where it snows most of the year to study snow mushi. He finds a boy with a strange affliction that causes snow to fall on him perpetually. He's become insensitive to the cold, and warmth is painful for him. It's dangerous for him to expose himself to the cold so much, but he doesn't even seem to care.

Ginko encounters a young woman being followed by a mysterious, watery creature. The woman becomes weak, and her family believes it to be lovesickness. Ginko reveals the truth of the mushi attached to her, but the woman must decide whether to give up her body to the mushi, or to dispel it and continue living.

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.

Ginko encounters Yuuta, a boy who is excellent at swimming and fishing but has webbed hands and cold skin. After discovering the boy's unnatural affinity for water, he sets out to treat the rain mushi causing his strange behavior.