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.

Rumors about a potential plot to dismantle the Shinsengumi by setting fire to their headquarters have spread amok. As most of the talk stems from an inn in Shimabara, the Shinsengumi place trust in Chizuru Yukimura for help with the investigation. Disguised as a geisha, Chizuru infiltrates the inn to provide intel for the Shinsengumi but quickly finds that the operation is more intricate than they could ever imagine. At the same time, each member of the Shinsengumi has their own reservations and concerns about using their sole female colleague to gather intelligence. Knowing what dangers await her, they all resolve to protect her at any cost.

Special episode included in the second Blu-ray/DVD volume.

Chibi-Earl and Chibi-Fairy. Every special focuses on another character, who will in their turn recite a poem by Shakespeare, that they feel describes their lives the best.