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The plot is set in Japan beginning from the 1990s and ending in modern day, with each segment centered on a boy named Takaki Tōno. It is important to remember that the first episode takes place during a time period when cell phones are uncommon and e-mail doesn't exist.
Episode 1: Ōkashō
Ōkashō (Cherry Blossom Extract): Takaki Tōno immediately befriends Akari Shinohara when she transfers to his elementary school. They grow closer to each other due to circumstances; for instance, they both prefer to stay inside during recess due to their seasonal allergies. Because of their similar interests and attitudes, over time they fall in love with each other, although due to their age it's debatable whether they themselves realize it. What is clear is that they form a unique and uncommonly strong bond. They even speak to each other using their given names without any form of honorifics, which is something very unusual in Japan even among people who are romantically involved. (This fact is unfortunately lost in the movie's translation to English and other languages, which significantly reduces the implied closeness between the two.)
Upon graduating from elementary school, Akari moves to Tochigi and Takaki moves to Tokyo due to their parents' respective jobs. The two keep in contact by writing letters, but despite the special feelings that exist between them, they inevitably begin to drift apart. When Takaki becomes aware that his family will be moving to Kagoshima, he decides to go see Akari since they will be too far apart to visit each other at all after he moves. However, when the day arrives, a severe snowstorm continually delays Takaki's trip, and it will be hours before he reaches the station where Akari is waiting for him. The two finally meet late that night and, as they share their first kiss, Takaki realizes that the two will never be together again. Stranded in a shed due to the snowstorm, the two fall asleep talking to each other late into the night. Takaki departs the next morning, and although they promise to continue writing each other, both silently acknowledge that their relationship with the other has effectively been ended.
Episode 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, has a strong crush on Takaki, but she does not have the courage to express her feelings to him. She spends all the time she can with him, even waiting long periods of time after school so they can walk home together. Any reasonable person would notice how obvious her feelings are for him, but Takaki seems blind to them, regarding Kanae as simply a good friend. Over time she observes that Takaki is always staring off into the distance, as if searching for something far, far away. Despite her feelings for Takaki, Kanae believes that he is searching for things far greater than anything she can offer. As in the first story, this segment concludes with Takaki again leaving his home behind because of his parents' jobs, apparently numb to any regrets for leaving Kanae or anyone or anything else behind.
Episode 3: Byōsoku 5 Centimeter
It is now 2008, and all three characters have gone their separate ways. Takaki is now a computer programmer in Tokyo, and Akari is preparing to get married. Kanae has presumably also moved on with her life. Takaki still seems to be longing for Akari to the detriment of his lifestyle and his other relationships, including a girlfriend he has been with for three years. Akari, while going through some old things, finds a letter she wrote to Takaki but never sent. She feels nostalgic for those days but has moved on with her life. On the verge of a breakdown, Takaki quits his job and tries to finally begin to take control over his life for the first time.
One day while walking down a road, Takaki comes to a railroad crossing. He passes a woman on the railroad crossing, and he stops on the other side of the tracks when he realizes what a strong resemblance she bore to Akari. He turns around to see that the person on the other side has also stopped and then also begins to turn around, but both are cut off from getting a good view of the other by two trains which cross on the tracks. Takaki waits for the trains to pass, expecting the woman he had seen to be waiting on the other side of the railroad crossing. After both trains have passed, he is disappointed to see that the woman is nowhere to be found. With a slight smile, he turns around and continues on his way.