The story centers around Amaya, Iwasawa, and Uehara—three "annoying, spirited high school girls with zero motivation"—and their classmates. Their daily life is "what happens when there is nothing happening." (Source: ANN)

The entire countryside comes to a halt midday to witness a rare solar eclipse that is rumored to allow the average person to see Mushi. Unable to avert their gaze, the air is full of awe and wonder—but those who know the Mushi are preparing for the eclipse's aftermath. Based on a prediction from Tanyuu Karibusa, the cursed recorder, Mushishi Ginko finds himself in a very unlucky farming village. Immediately following the solar eclipse, a strange black cloud begins to gather in the sky and blocks the sun once more. Suspecting it to be the work of a Mushi known as Hihami, Ginko seeks to liberate the village from perpetual darkness. However, it seems that not all of the villagers are eager to return to the light.

In a world inhabited by people only a few inches tall, young women Hakumei and Mikochi live together in a house built into a tree. Hakumei is an energetic and tomboyish carpenter, while Mikochi is a feminine and calm tailor. Despite their differences, they get along well and spend their days having fun living their lives in the woods. The two of them spend their time working, going on sightseeing adventures, and taking shopping trips into Tsumiki Marketplace by the ocean. They make many friends along the way, be they sentient woodland creatures like Iwashi the Weasel or fellow miniature people such as the songstress Konju and the inventor Sen. Hakumei to Mikochi is a relaxing look into the day-to-day lives of its titular characters as they explore and interact with their tiny world which seems to be straight out of a fairy tale. [Written by MAL Rewrite]