Ginko, a Mushi master, travels from place to place researching the Mushi and helping people who are suffering because 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.
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.