Umi Matsuzaki is a 16-year-old high school student residing in Coquelicot Manor, a boarding house perched above the bustling Port of Yokohama in Japan. Her mother, Ryoko, a medical professor, is currently studying in the United States, leaving Umi to manage the household and care for her younger siblings and grandmother. Every morning, she diligently raises a set of signal flags that convey her heartfelt message: “I pray for safe voyages.”
One day, Umi’s flags capture the attention of the talented poet, Shun Kazama, whose poem about the flags is featured in the Konan Academy newspaper. As Shun rides his father's tugboat to school, he spots the flags. Initially, Umi mistakes Shun for a reckless daredevil when he performs a stunt for the "Latin Quarter," an old building that houses their school's clubs, now facing the threat of demolition. At her sister's urging, Umi ventures to the Latin Quarter to get Shun’s autograph and discovers that he, along with the student government president, Shirō Mizunuma, also helps publish the school newspaper. Umi persuades them to lead a renovation of the Latin Quarter, encouraging all students—boys and girls alike—to contribute, and soon, feelings blossom between Umi and Shun.
In a touching moment at Coquelicot Manor, Umi shares a photograph of three young naval men with Shun. To her shock, one of the men is her late father, Yūichirō Sawamura, who tragically lost his life while serving on a supply ship during the Korean War. Shun reveals that he possesses a similar photograph and learns that his father had taken him in after Yūichirō, who had been traveling with an infant, was brought to their home shortly after World War II. As Shun grapples with this revelation, he eventually confesses that they are siblings. Despite their initial romantic inclinations, Umi and Shun suppress their feelings, opting to remain friends.
As renovations to the Latin Quarter progress, the Kanagawa Prefectural Board of Education decides to proceed with the building's demolition. In a daring move, Umi, Shun, and Shirō embark on a trip to Tokyo, bustling with preparations for the 1964 Summer Olympics, to convince Tokumaru, the board's chairman, to inspect the Latin Quarter. Their efforts pay off when Tokumaru is impressed and ultimately decides to halt the demolition plans. In a vulnerable moment, Umi admits her love for Shun, who reciprocates despite the complications arising from their familial ties.
Upon her return from the United States, Ryoko reveals even more shocking truths: Shun’s father was actually Hiroshi Tachibana, the second man in the photograph, who perished in an accident during a rush to return home in 1945. Shun’s mother died during childbirth, leaving him orphaned after the tragic bombing of Nagasaki. Unable to raise Shun due to her own pregnancy with Umi, Ryoko explains how Yūichirō had registered Shun as his own child to prevent him from becoming an orphan during the chaotic postwar era. Ultimately, Shun was adopted by the Kazama family.
In a thrilling climax, Tokumaru visits the Latin Quarter and, impressed by the students’ dedication, cancels the demolition order. Umi and Shun are invited to the harbor, where they meet Yoshio Onodera, the last man remaining from the photograph and now a ship's captain. He confirms that Umi and Shun are not biologically related and shares the poignant history of the three men. With their identities and relationships finally clarified, Umi returns to her daily ritual of raising the signal flags, now carrying a deeper meaning as she sends her prayers not just for her father, but for the connections they have all forged.
