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.

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.

"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".

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?

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

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?

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.

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.

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.

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.

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".

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.

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 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.

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."

"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.

"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.