Mushi: the most basic forms of life in the world. They exist without any goals or purposes aside from simply being. They are beyond the shackles of the words good and evil. Mushi can exist in countless forms and are capable of mimicking things from the natural world such as plants, diseases, and even phenomena like rainbows. This is, however, just a vague definition of these entities that inhabit the vibrant world of Mushishi, as to even call them a form of life would be an oversimplification. Detailed information on Mushi is scarce because the majority of humans are unaware of their existence. So what are Mushi and why do they exist? This is the question that a Mushishi, Ginko, ponders constantly. Mushishi are those who research Mushi in hopes of understanding their place in the world's hierarchy of life. Ginko chases rumors of occurrences that could be tied to Mushi, all for the sake of finding an answer. It could, after all, lead to the meaning of life itself.

With another Wave happening in a week, Naofumi Iwatani and his party have no time to waste. However, when bat familiars raid Lurolona Village and the Wave countdown comes to a halt, the Four Cardinal Heroes reconvene with the queen, Mirelia Q Melromarc, for a quick briefing. The queen presumes that the odd occurrences are linked to the Spirit Tortoise—a threatening creature that has awakened from its slumber, back to cause havoc once again. A plan to put the Spirit Tortoise to rest is devised—but out of the four men, only the cursed Shield Hero agrees to help.

Traveling merchant Kraft Lawrence continues his northward journey with wolf goddess Holo, in search of her lost home of Yoitsu. Lawrence and his sharp-witted partner continue to make some small profits along the way, while slowly uncovering more information about Holo's hometown. However, the road to Yoitsu is a bumpy one filled with many troubles—Lawrence runs into a charming young fellow merchant who has his eyes set on the female wolf companion, and he begins to doubt if Holo will remain by his side; he and the goddess will also have to consider precarious and risky business deals as Lawrence strives to achieve his dream of becoming a shopowner. All the while, with his determination tested at every turn during his journey, Lawrence must question his relationship with Holo, take on business ventures, and ask himself whether it is time for him and Holo to go their separate ways.

Yoshino Takigawa, an ordinary teenager, is secretly dating his best friend Mahiro Fuwa's younger sister, Aika. But when Aika mysteriously dies, Mahiro disappears, vowing to find the one responsible and make them pay for murdering his beloved sister. Yoshino continues his life as usual and has not heard from Mahiro in a month—until he is confronted by a strange girl who holds him at gunpoint, and his best friend arrives in the nick of time to save him. Yoshino learns that Mahiro has enlisted the help of a witch named Hakaze Kusaribe to find Aika's killer. However, the witch has been banished to a deserted island due to infighting within her clan. Hakaze's brother, Samon, selfishly desires to make use of the Tree of Exodus' power, in spite of both his sister's opposition and the impending peril to the world. With Hakaze out of the picture, it is now up to Yoshino and Mahiro to help her save the world, all while inching ever closer to the truth behind Aika's death.