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!

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.

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 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...

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.

Ginko is waiting along the sea shore, for a transport to get him across the bay when he meets a man called Shirou, who lost his wife under strange circumstances. Ginko seems interested and decides to listen to his story about how he lost his wife in a swarm of sea snakes, during fog. Ginko later comes back with information on the Mushi that caused the bizarre events.

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.

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".

While resting in a bamboo forest, Ginko is approached by an odd man named Kisuke, who tells Ginko that he has been lost in the forest for 3 years. Ginko seems to have also become lost, and decides to go off and figure something out about the forest. After managing to get out of the forest, Ginko figures out that it's the work of a "Magaridake".

"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.

"There are countless fissures in the physical world. Those who vanish like smoke are lost in such hollows. Without their memories, without their souls..." Ginko receives a letter in a cocoon, but it isn't adressed to him. Rather, it's addressed to an old accquaintance, Aya Tozawa, so he decides to visit her. Ginko is concerned about Aya, as she is still searching for her sister, who has been trapped in an Uroana for 5 years.

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.

Seijirou is fascinated by the stars and enjoys stargazing. One day he was by the riverbed with the village nanny Fuki when she notices a string coming down the sky and as she tries to pull all of a sudden she disappears, right before Seijirou's eye. Ginko is travelling through the mountains and is being followed by a peculiar girl. It turns out that it's Fuki, who has been exposed to a strong Mushi presence and can't be seen by anyone.

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.

A lady named Aki discovered a green stain on her wedding gown, one year later she gave birth to a boy who, now grown up, has the same marks on his body. It turns out that the boy was originally born not as a human but as some shapeless green blob, which then turned into a human. Her husband asks for Ginko's help yet he is unable to save her son because it's the work of a "Watahaki".

"Give birth to me once more. I want to meet you once more. I want to see this beautiful ocean once more..." Ginko arrives on an island asking about the so called "Rebirths" but to no luck. At night he later meets a peculiar lady who happens to be able to see a strange light in the sea and she ends up inviting him to her home. She later explains to him what "Rebirths" are; when a person is about to die they can be taken deep inside the Ryuugu, where they are reborn.

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.

"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.

"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.

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?

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.

A young man has the power to lure animals to him using a scent issuing from his hand. He inherited this power from his father, and it makes hunting easier. But it makes the meat from his prey taste foul. More serious is the risk of losing his mind to the power and confusing family with prey. There's a cure, but will the boy be willing to give up his power?

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.

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.

A woman afflicted by a water-type mushi decides to make use of her condition to help those in need.

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 falls unconscious on a snowy mountain. He is helped by locals who somehow manage to grow their fields despite the weather, mainly because of a worker with unabated stamina. But at what cost does this vigor come?

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?

After his encounter with Nui and before becoming a mushishi, young Ginko moved from place to place, due to his condition of attracting mushi. At one point he found himself instructed and cared for by a mushishi named Suguro, in the lands of a dying Mountain Lord. Ginko wonders about his place in the world and the natural order, as Suguro worries that the new Mountain Lord hasn't yet appeared.

A man feels something vaguely familiar, yet terrifying, as he smells the scent of flowers at night. As an old man, walking through the woods, he finds a tunnel, and is compelled to enter it. While going through it, he reminisces about important events in his life up to that point, but it seems there is something he can't quite recall. Perhaps long ago, the visit of a traveler looking for shelter on a rainy day, might help shed light on the unsettled feeling he has.

At dusk, about to go home after playing with her friends, a young girl named Akane found a shadow without a caster. On that same day, she disappeared. Several years later, Ginko is told the story of Mikage, a girl who appeared with no memories at Akane's village shortly after the vanishing of the latter.

Yura and Sumi, the former's caretaker, were close friends. Eventually, as they were moved apart, Yura could still feel Sumi's presence. However, whenever that happened, she'd become like an empty shell, worrying her father. As Ginko comes to know of the case, he proceeds to offer them advice, as the condition is caused by a mushi that can connect people's minds.

A young boy named Gen troubles his father by being too rough with other kids, who pick on him due to his absent mother. The child, too strong for his age, also claims to be able to see strange creatures that no one else sees. As Ginko arrives at Gen's place, the story behind Gen's strength is revealed as the mushishi recounts the day he met a woman who'd woven a mysterious seamless garment.

Izumi is alone in a world that mirrors our own. Having forgotten how she came to be there, she remains trapped while her family searches in vain. Her father believes she has been kidnapped, while her mother and sister Mizuho believe that she is still inside the house, even though they cannot see her. Ginko crosses into the other world to try to save her.

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.

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.

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.

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.