5 Centimeters Per Second

The story is set in Japan beginning from the 1990s and ending in modern day, with each act centered on a boy named Takaki Tōno. The first act takes place during a time when cell phones are uncommon and email has not yet reached the general population.

Act 1: Cherry Blossom

Takaki Tōno quickly befriends Akari Shinohara when she transfers to his elementary school. They grow closer to each other due to similar interests and attitudes; for instance, they both prefer to stay inside during recess due to their seasonal allergies. As a result, they form a strong bond; they speak to each other using their given names without any form of honorifics, which is a sign of deep friendship and familiarity in Japan. (This fact is lost in the movie's translation to English and other languages, which reduces the implied closeness of their relationship.)

Upon graduating from elementary school, Akari moves to Tochigi, due to her parents' jobs. The two keep in contact by writing letters but eventually begin to drift apart. When Takaki learns that his family will be moving to Kagoshima, he decides to personally go see Akari, since they will be too far apart to visit each other at all after moving. He also prepares a letter for Akari, containing his feelings. However, during the journey he loses the letter and a severe snowstorm continuously delays Takaki's trip for several hours. As the two meet and share their first kiss, Takaki realizes they will never be together again. Stranded in a shed due to the snowstorm, they fall asleep after talking late into the night. Takaki departs the next morning, and they promise to continue writing to each other. As the train rolls away, Takaki thinks that the loss of his letter is not important any more after that kiss, while Akari silently looks at her own letter addressed to Takaki.

Act 2: Cosmonaut

Takaki is now in the third year of senior high in Tanegashima, where the Tanegashima Space Center is located. Kanae Sumida, a classmate of Takaki, had fallen in love with him ever since meeting him in middle school but does not have the courage to confess her feelings. She tries to spend time with him, waiting long after school for the chance to travel home together. However, Takaki appears ignorant to Kanae's feelings and treats her as a good friend. Kanae observes that Takaki is always writing emails to someone or staring off into the distance as if searching for something far, far away. It is later shown that Takaki's emails are not being sent to anyone, and he has had recurring dreams which feature Akari. Despite Kanae's feelings, she eventually realizes that Takaki is looking for something far beyond what she can offer and decides against telling him how she feels.

Act 3: 5 Centimeters Per Second

It is 2008. Takaki is now a computer programmer in Tokyo, and Akari is preparing to get married. Kanae is not strongly depicted in this segment. Takaki is still longing for Akari to the detriment of his lifestyle, which is acknowledged by an ex-girlfriend. This leads to Takaki on the verge of a breakdown and leaving his job. Akari goes through her old possessions and finds the letter addressed to Takaki. Takaki and Akari have a dual narration, both recalling a recent dream depicting the events of their last meeting in the snow and hoping to watch the cherry blossoms together again.

One day while walking down a road, Takaki and Akari appear to pass and recognize each other at a train crossing, where they decided to watch cherry blossoms together right before Akari's sudden moving to Tochigi thirteen years ago. At opposite sides of the tracks, they stop and begin to look back, but the passing trains cut off their view. Takaki waits for the trains to pass but sees that Akari is gone. After a moment, he smiles to himself and continues walking.