Gen Kudou, a koto maker, believes that his delinquent grandson Chika would never understand the profoundness of the traditional musical instrument. In an attempt to make up for his naivety and understand the words of his late grandfather, Chika tries to join the Tokise High School Koto Club. Even though the club is in dire need of members, new club president Takezou Kurata is unwilling to easily accept Chika's application due to his bad reputation. Nonetheless, after seeing Chika's seriousness and enthusiasm, Takezou allows the problem child to join, along with koto prodigy Satowa Houzuki and three of Chika's energetic friends. Kono Oto Tomare! follows the merry band of musicians as they aspire to play at the national competition.

Atop a hill overlooking a seaside port sits a boarding house named Coquelicot Manor. Since the building is run by her family, Umi Matsuzaki carries out many of the duties involved in managing the small establishment, such as preparing meals for her fellow boarders. When she isn't at home, she is a student at the local high school—one that is currently dealing with a small crisis. In anticipation of the upcoming Olympic Games, a beloved old clubhouse is set to be demolished to make way for a modern building. As a result, a large part of the student body has banded together, working tirelessly to prevent this from happening. Umi finds herself helping the newspaper club to spread information about this cause where she befriends Shun Kazama, whom she gradually begins to fall in love with. But Shun is an orphan who doesn't know much about his origins, and when the two begin searching for clues to the boy's past, they discover that they may have a lot more in common than either of them could have thought. [Writtten by MAL Rewrite]

Having been best friends since middle school, Haruka Takayama and Yuu Sonoda plan to attend Misato West High School together. However, despite being assigned to the same class, a cruel twist of fate has them seated on the opposite ends of their classroom! To make matters worse, their school will shut down in three years, making them the final intake of first-year students. Undeterred by this chain of unfortunate events, Haruka is set on sticking with Yuu, striving to create many wonderful memories with her. Much to Haruka's jealousy however, Yuu's easygoing demeanor quickly attracts the attention of their female classmates. Sympathizing with her friend's growing insecurity, Yuu ends up sharing a deep, affectionate kiss with her in an empty classroom. The act intensifies their bond as special friends, gradually revealing a different aspect to their unique friendship while also inviting new conflicts.

The true end arc of Ore no Imouto. These four episodes branch out after the 11th episode of the main TV series and present an alternative version to the end of the TV series. These episodes contrast with the good end arc of the TV series, which was an original ending written for the anime, and instead closely follows the original story from the light novels.