In the countryside village of Asahigaoka, a fifth grade elementary school girl named Hotaru Ichijou moves in from the city and transfers into the village’s branch school, which consists of only four other students; a first grader named Renge Miyauchi and three middle school siblings, Natsumi, Komari and Suguru Koshigaya, along with their teacher, Renge’s older sister Kazuho. After school, Renge invites Hotaru and the others to her house, where she shows off her pet tanuki. The next day, the girls take Hotaru to a blooming cherry blossom tree to eat their sakuramochi, though they end up missing the bus home on the way back.

Ichijou Hotaru is enjoying life with her classmates at her new school. In particular, she has come to think of the diminutive Koshigaya Komari, at less than 140cm, as her “cute Senpai.” This feeling soon grows into absolute adoration. Then, one day, Komari calls Hotaru and invites her to hang out together…

The class goes on a school trip to help out in a rice field, where Natsumi and Komari end up getting stuck in the mud. Later that night, Komari gets frightened after seeing a scary movie, which is not helped by Natsumi. After getting into a fight with her mother, Natsumi runs away from home with Komari in tow and goes to her secret hideout. They eventually spot a cat that had put Natsumi in trouble in the first place, but leave her alone when they see she is feeding her family and eventually head home.

As summer vacation begins, Renge’s older sister Hikage comes home from her school in Tokyo, hoping to impress the others with her know-how about city life only for Hotaru to outshine her. Later, Renge meets another girl her age named Honoka Ishikawa, who she quickly become friends with. After spending several days playing with Honoka, Renge is saddened when she learns Honoka had to suddenly leave due to her father’s work. However, she cheers up a week later after receiving a letter from Honoka saying she’ll come back next summer.

Hotaru and Renge are invited to the Koshigaya’s house for breakfast. Afterwards, the girls, accompanied by Kazuha, go to the beach, where Komari’s height leads her to be mistaken for a lost child. On their way home, the girls stop at a railside noodle restaurant, where a prank by Natsumi on Komari backfires due to Renge’s innocence. They manage to catch the last train home on time, but accidentally leave Kazuha behind.

Natsumi gets chewed out by her mother over her poor school grades whilst also trying to hide her poor test results from her. Afterwards, the girls visit Hotaru, who attempts to hide the vast number of handmade Komari plushies in her room. This ultimately fails, but she manages to pass them off as part of a school project. Later that night, the gang have a test of courage at the shrine, which proves a bit too much for Komari.

With Kazuha absent at the start of the new semester, the girls try and find ways to pass the time in class. Later, Hotaru and Renge try and catch a rabbit that had escaped from its pen, only for it to lock them inside the pen themselves, though they are eventually rescued by Kazuha. Afterwards, Renge visits the candy store run by Kaede Kagayama, who finds her to be a handful.

Hotaru gets along with the Koshigaya family’s next door neighbour, Konomi Fujimiya, whilst Komari laments that the two seem more grown up than she is. Later, Komari joins Hotaru and Renge in doing some sketching, where she ends up becoming a model for them. Afterwards, Konomi helps Komari and Natsumi make dried persimmons.

Since the school doesn’t hold cultural festivals, Natsumi suggests they hold their own and invite the alumni, including Kaede, Konomi and Hikage. At the festival, the girls run a café, hold an art exhibit and put on a play. However, they’re play ends up being overwhelming and they end up slacking on food orders. They do eventually work together to prepare some food and have fun. Afterwards, Komari and Konomi help clean Natsumi’s room, where they find a lot of old toys.