Keitaro and his childhood sweetheart make a promise to be accepted at and to meet each other at the prestigous Toudai University before she moved out of his life. About a decade later, Keitaro has become an artist and a daydreamer, having ranked 27th from the last in the national practice exam. When his grandmother leaves the all-girls dormitory, he becomes the residential manager and soon meets up with two Todai applicants who may have been that sweetheart, since he`s forgotten her name. Then there the other tenants like young Shinobu who was in despair until Keitaro helped her, Motoko the swordsmaster who sees men as evil distractions, Su Kaolo the genius child inventor and the sneaky Kitsune.

The story centers around Yoshizou Yukawa, a major hot spring fan who finds hidden springs to revitalize the economy of the local area. However, he dies after falling off a cliff and is transported to an alternate world, thanks to an inari deity of harvest at a small shrine nestled in the rocks. Together with the inari's attendant princess Mayudama, he continues searching for storied hot springs, only this time in the alternate world. Along the way, he ends up naked in hot springs with furry-eared girls and elven girls.

Konohana Kitan is the heartwarming story of a new apprentice named Yuzu, and the other fox girls who work at a hot spring hotel called Konohatei. The staff at Konohatei live by one belief: no matter who one may truly be, no matter what, anyone who is a guest is a god. Of course, that includes you. Let the hospitality of Yuzu and the Konohatei heal your tired soul.