The story of the film begins after the events of the second season, at the graduation ceremony of the third-year students. Knowing that the graduation of the third-year members means the end of u's, the nine girls take a walk around the school filled with memories. However, when the students attempt to leave the school gates, a single email is sent to them, and the curtain on a new story for u's begins.

Twenty-six years ago, in a third-year classroom of a middle school, there was a student named Misaki. As an honors student who was also good at sports, the charming boy was popular with his classmates. When he suddenly died, his classmates decided to carry on as if he was still alive until graduation. Then, in the spring of 1998, a boy named Sakakibara Kouichi transfers to that classroom, and he grows suspicious of the fearful atmosphere in that classroom. In particular, there is a beautiful, aloof girl named Mei Misaki who wears an eye-patch and is always alone drawing pictures. Written by (Summaries provided by ANN and AniDB)

Twenty-six-year-old Hiroto Suwa; his wife, Naho; and their old high school classmates—Takako Chino, Azusa Murasaka, and Saku Hagita—visit Mt. Koubou to view the cherry blossoms together. While watching the setting sun, they reminisce about Kakeru Naruse, their friend who died 10 years ago. Mourning for him, they decide to visit Kakeru's old home, where they learn the secret of his death from his grandmother.