In a bustling village of spirits, Yuzu, a cheerful fox girl, starts her first job as an attendant at the traditional hot springs inn Konohanatei. Though Yuzu has no experience working at such a high-class establishment, Kiri, the affable and reliable head attendant, immediately puts her to work learning the basics. While Yuzu's eagerness initially proves to be more of a hindrance than a blessing, her playful nature brings a unique charm to the inn, as both customers and her fellow workers quickly warm up to her clumsy yet well-meaning mistakes. Under the guidance of the other foxes—the rigid Satsuki, the carefree Natsume, the critical Ren, and the quiet Sakura—Yuzu steadily learns the trade of an inn attendant while learning to love the magical world surrounding her. Konohana Kitan presents the heartwarming tale of a simple fox girl forging bonds with others and finding a home amidst the mysterious, beautiful world of spirits.

After surviving a brutal terrorist attack on Plant Quetta, Suletta Mercury returns to dueling at the Asticassia School of Technology, while Miorine Rembran sits at her injured father's side, waiting to see if he will recover. As the residents of Earth House are preoccupied with their respective troubles, two members of Dawn of Fold—the perpetrators of the attack—secretly infiltrate the school, putting Suletta and her friends at risk. At the same time, Prospera, Suletta's mother, approaches Miorine to propose the continuation of Quiet Zero—a project headed by Miorine's father that can allegedly end all war. Prospera seems to be another political figure with hidden, opposing motives, and whether she truly has Suletta's well-being at heart remains to be seen.

After leaving her idol career behind, Fuuka Miyazawa finds herself on a spontaneous flight to Okinawa instead of returning home to her pity party in Morioka. Bearing a heavy heart and nowhere to go, she aimlessly wanders around the area until she stumbles upon Gama Gama Aquarium—an aging aquarium on the verge of closing down. With a lack of visitors and costly but necessary repairs needed to keep its doors open, the director is faced with shutting down the establishment for good by the end of the summer. The director's aquatic life-loving granddaughter—Kukuru Misakino—cannot stand the thought of the aquarium closing and is determined to make enough money by the end of the season to keep the doors open. Seeing the unique magic of the aquarium, Fuuka begs Kukuru for a job; however, she soon finds that her lack of experience makes her more of a hindrance than anything else. At the same time, Kukuru realizes that her ambitious goal might be more than she can handle. With mounting pressure from all around them, will Kukuru and Fuuka be able to save the one place they hold close to their hearts?

Naoya Mukai's crazy lifestyle of balancing his time between both of his girlfriends, Saki Saki and Nagisa Minase, is still as hectic as ever. Additionally, the blonde bombshell Rika Hoshizaki also has her sights on Naoya, complicating his already convoluted love life. As if things could not get more ridiculous, another girl inserts herself into the situation: Shino Kiryuu, who is determined to end Naoya's two-timing and ensure Saki's happiness. However, Shino harbors secret feelings for Naoya—a longing she believes she must forsake—yet simply cannot due to the deep attraction he inspires.