The short movie comes in three linked segments, or as the movie's subtitle puts it, "a chain of short stories about their distance." In the first, "The Chosen Cherry Blossoms", two elementary-school students become fast friends, and something more. Takaki Tonho and Akari Shinohara meet as children in Tokyo, enduring some teasing because of their relationship but shrugging aside other people in order to live in their own little world. Then Akari's parents move far across Japan. While they continue writing to each other, it's difficult to visit, but when he realizes his own parents are planning a move that would put even more distance between them, Takaki travels to meet Akari, and they kiss for the first time.

In the second chapter, "Cosmonaut", Takaki is in high school, and his classmate Kanae has fallen in love with him. But she finds him unapproachable, as he always seems focused somewhere far away. Living in the shadow of Tanegashima Space Center, where a new launch is being prepared, the two of them contemplate the enormous distances cosmonauts travel, and how much shorter distances can still keep people apart. In Kanae and Takaki's case, even physical proximity can't bridge the profound gaps between them.

Finally, in a third chapter, "5 Centimeters Per Second", an adult Takaki works in Tokyo and contemplates his life and how his feelings have developed over the years.