Bộ phim gồm 3 phần, chủ yếu kể về chuyện của 2 người wa từng giai đoạn. Tohno Takaki và Shinohara Akari, đã từng là bạn thân nhưng mọi chuyện dần thay đổi theo dòng thời gian.
Part 1 - The Chosen Cherry Blossoms (26 min): Because of family movement, Shinohara Akari had leave Tokyo upon graduation from elementary school. The deep feelings between Takaki and Akari for each other keep them in contact, but they worry they may not meet again. Then, one day, Takaki learns that his familiy will move from Tokyo to an island in the far south of Japan, so he decides to use this last opportunity visit Akari by train...
Part 2 - Cosmonaut (21 min): Years have passed, and Takaki still writes eMails aimed at Akari, only to never send them to her. Meanwhile Sumita Kanae, his classmate, has special feelings for Takaki, but she does not have the courage to express her love to him...
Part 3 - 5 Centimeters per Second (16 min, more of a music clip than anime): Takaki is working as computer programmer now, occasionally remembering his former life - and love. And then, at a railroad crossing he suddenly passes by a woman who looks familiar to him...