Koguma, a reserved second-year high school student, has nothing—no parents, hobbies, friends, or goals. On her way home one afternoon, she visits a vehicle shop in hopes of acquiring a motor scooter. With only enough money to make ends meet, she is disheartened by the price tags and prepares to turn back. However, as she is about to leave, the shop's owner offers her a pre-owned Honda Super Cub for ten thousand yen. Believing that the motorcycle will help brighten her monotonous world, she accepts the deal. As Koguma journeys through her town on small adventures with her Super Cub, she begins to build irreplaceable friendships and eagerly advances toward her new life.

Takuma Hirose is a blind young male high school student, though the cause for his blindness is undetermined. In order to heal his medical condition, he is sent to live in a village with his uncle. There, he meets several girls, three of which stand out more than any of the others. They are Hayami Kohinata, Hinata Kangura, and Otoha. Otoha temporarily heals his blindness and Hirose uses his sight to help others. He finds out that, for some reason, Hayami Kohinata is hated in the village, and he tries his best to help her out. Meanwhile, many sad secrets unfold in the village...

Tired of her rural home, recent college graduate Yoshino Koharu is desperate to lead a more exciting life in Tokyo. After a fruitless job hunt, she finally receives a part-time offer as queen of the bizarre Kingdom of Chupakabura, a rundown mini-attraction in the small agricultural town of Manoyama. However, Yoshino discovers upon her arrival in Manoyama that she was mistaken for a celebrity and the job offer was a mistake. Left with no other options, Yoshino reluctantly agrees to take on the role and aid the Board of Tourism in their efforts to revitalize Manoyama. Determined to bring excitement to the dying town with the help of local residents, the queen enacts a series of projects to highlight the beauty and charm of Manoyama's culture. Sakura Quest delves into the story of a tight-knit community that is struggling to balance change while also maintaining the rich traditions and bonds which define their identity.

Rika Furude and Satoko Houjou are best friends who have lived in the small village of Hinamizawa for their entire lives. Alongside their other friends, they spend every day together, and every moment is filled with fun and laughter. However, as Rika and Satoko begin to grow older, a life-changing opportunity presents itself to both of them. Rika is determined to follow her dreams and wants Satoko by her side. Although Satoko is hesitant, she decides to walk this path with Rika. However, the realization of her dream forms a rift between them. This leaves the girls living in completely different worlds, with Rika enjoying her new life and making new friends while Satoko grows more and more isolated. Longing to return to the nostalgic days in Hinamizawa, Satoko despairs and wishes things could be changed. Just when she is at wits' end, an encounter with a supernatural entity changes Satoko's perception and imparts new revelations about her best friend Rika. This begins her journey to get the future she desires—by any means necessary.