Umi Matsuzaki is a 16-year-old high school student living in Coquelicot Manor, a boarding house overlooking the Port of Yokohama in Japan. Her mother, Ryoko, is a medical professor studying in the United States. Umi runs the house and looks after her younger siblings and her grandmother. Each morning, Umi raises a set of signal flags with the message "I pray for safe voyages".

One day, a poem about the flags being raised is published in Isogo High School's newspaper. Shun Kazama, the poem's author, witnesses the flags from the sea as he rides his father's tugboat to school. At first, Umi gets the wrong impression of Shun as he does a rash stunt on behalf of the "Latin Quarter", an old building housing their high school's clubs that's being threatened with demolition. Upon her sister's request, Umi accompanies her to obtain Shun's autograph at the Latin Quarter. She learns that Shun and the school's student government president Shir? Mizunuma publish the school newspaper. Umi convinces Shir? and Shun to renovate the Latin Quarter, and all the students contribute, both boys and girls. Umi and Shun start having feelings for each other.

At Coquelicot Manor, Umi shows Shun a photograph of three young naval men. One of these men is her deceased father, Y?ichir? Sawamura, who was killed while serving on a supply ship during the Korean War. Shun is stunned to see it as it is revealed that he has a duplicate of the photograph. His father admits that, shortly after the end of World War II, Y?ichir? arrived at their house one evening with an infant Shun. The Kazamas had recently lost a newborn baby, so they adopted Shun. At first, Shun tries to avoid Umi, then finally tells her they are siblings. Umi and Shun repress their romantic feelings and they continue to see each other as friends.

The renovation of the Latin Quarter is complete but the Kanagawa Prefectural Board of Education decides to proceed with the building's demolition anyway. Shir?, Shun and Umi take the train to Tokyo, which is preparing for the 1964 Summer Olympics, and meet with Tokumaru, the school board's chairman. They successfully convince him to come inspect the Latin Quarter. Umi later professes her love to Shun, and he reciprocates in spite of their situation.

Having just returned from the United States, Ryoko tells Umi that Shun's father was actually Hiroshi Tachibana, the second man in the photo. In 1945, Tachibana was killed in an accident on a repatriation ship. Shun's mother died in childbirth, and his other relatives were killed in the bombing of Nagasaki. Ryoko was unable to raise Shun, as she was already pregnant with Umi at the time. Y?ichir? registered the child as his own to avoid leaving Shun as an orphan in the confused postwar years, but Shun was eventually given to the Kazamas.

Tokumaru visits the Latin Quarter and, impressed by the students' efforts, cancels the demolition. Umi and Shun are summoned to the harbor. They meet Yoshio Onodera, now a ship's captain and the third man in the photograph, as well as the sole survivor of the three. Confirming that Umi and Shun are not related by blood, he tells the full story of the three men. With everything resolved, Umi resumes her daily routine of raising the flags, but now, it is not just for her father.

https://en.wikipedia.org/wiki/From_Up_on_Poppy_Hill
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