In 1918, Jiro Horikoshi is a young Japanese boy growing up with his mother and young sister. Jiro has very poor eyesight (hence his Coke bottle style glasses), which gets in the way of his dream to become a pilot. He spends much of his time reading aviation magazines and fending younger kids off from bullies at school. One night Jiro has a vivid dream of Giovanni Battista Caproni, an Italian aeronautical engineer. Caproni becomes his mentor and friend in following dreams, and Jiro begins to notice that the man loves building planes, but that he frowns upon the use of "beautiful dreams" for war or violence.
Fast forward about eight years or so, and Jiro is a young adult, on his way by train to university, where he'll study to become an engineer. While riding outdoors, the wind lifts his hat up off his head, where a beautiful young girl catches it. She's there with her maid, and they exchange a friendly greeting with Jiro, but don't give their names. Soon after, the town they're riding through is hit by a brutal earthquake. The girl's maid breaks her ankle and can't walk, so Jiro offers to carry her away from the de-railed train before the ensuing explosion and fire can hurt them. He leaves soon afterwards without giving his name. Through engineering school, Jiro acts somewhat eccentric, eating fish every day just so he can study the curve of the bones and not socializing much. He eventually befriends Honjo, a fellow student. Meanwhile his little sister, Kayo, decides she'd like to go to medical school, training to become a doctor. Jiro receives a package at school wrapped in purple cloth, which he discovers is his slide ruler that he used to brace the broken ankle of the woman he saved during the earthquake, as well as his shirt, which he brought water in. Realizing that it must've been the girl and her maid from the train who dropped it off, he rushes into the street to thank them, but there's no sign of them being there.
In 1927, Jiro is hired at the Mitsubishi Corporation to design a more compact, modern and streamlined fighter jet. He has no idea how the planes will eventually be used, but remembering Caproni from his dreams, he dedicates his skills wholeheartedly. His boss, a curmudgeonly dwarf named Kurokawa, at first finds him foolish but soon develops a fondness for him thanks to his intricate airplane designs. Honjo, also employed at the corporation, remains a close friend to Jiro, and together they work on the Falcon, the fighter plane that will supposedly aid them in bring peace by helping in the war effort. Bothered somewhat by the implications of this, Jiro finds himself looking to Caproni for guidance more often. During a test flight, the Falcon breaks apart in mid-air, and Jiro becomes frustrated by Japan's backwards technology, which utilizes mostly wood and canvas instead of metal. Him and Honjo are sent to Germany together to learn about the fellow country's modern technological advancements.
Germany seems radically different from the quaint atmosphere of Japan. Jiro and Honjo are amazed by the Junkers G.38, an airplane made entirely from lightweight metal. While at the factory where it's being stored, they're surprised to find that the German guards are incredibly hostile towards them both, however Hugo Junkers, the owner, cheerfully allows them aboard the new plane. Jiro marvels about how many people the plane could hold, and he thinks it could have much better purposes than for use in the war. He dreams again of Caproni, who tells him that the world is a better place because of planes, but that mankind will inevitably use them for sinister purposes if they feel like they can win with them.
Jiro and Honjo return to Japan. Jiro begins working with Kurokawa on a new fighter plane, plus he gets promoted to chief designer. Again his designs fail, much to his disappointment. In 1933, he spends his summer at a hotel resort in rural Japan, where he runs into a familiar-looking young lady. While out painting, she loses her umbrella in the wind, but Jiro catches it and returns it to her grateful father. The girl, whose name is Nahoko, turns out to be the girl whose maid was saved by Jiro during the earthquake. Nahoko reveals during a walk through the rain with Jiro that the maid now has two children, and that she cried with joy upon learning what Jiro's real name was during the time that he was in engineering school. Jiro and Nahoko befriend a kindhearted piano player, Mr. Castorp, another guest at the hotel. Castorp, secretly a Soviet spy who fled from Germany, admits to Jiro that he disapproves of the Nazi Regime's cruelty and carelessness, and also warns him that Junkers, the airplane factory owner from Germany, is in grave danger for going against Hitler's views on war and the Holocaust. Soon after, Jiro gets permission to marry Nahoko despite her tuberculosis.
Returning to his career, Jiro is told by Kurokawa that the Japanese Secret Service is seeking him out as an enemy of their German allies. Several of Kurokawa's friends have also been arrested, so Jiro goes to live at his boss' house until the suspicion dies down. He writes to Nahoko, and discusses with her how Mr. Castorp was wanted for being a traitor to Germany. He prays their friend has escaped the country safely, knowing what sort of fate would await him if he were caught. Nahoko comes to visit the Kurokawa household, where reluctantly Mr. Kurokawa weds them both in a traditional ceremony. Kayo, now a doctor, visits her brother, but cautions him that the marriage is ill-advised because of Nahoko's likely short life she has left. As Nahoko gets more sick, she still continues to enjoy her time with Jiro, and she and Kayo even become close friends. While Jiro returns to work, finally creating a successful design, Nahoko passes away in a sanitarium.
In 1945, Jiro's design for the "Mitsubishi Zeroes" is used, but much to his horror, he discovers that the planes are used for suicide missions by Kamikazes. In his dreams, he is haunted by the sight of thousands of the ruined planes being destroyed in fiery explosions, much like Caproni was haunted that his Italian aircraft designs were used for mostly destructive purposes. Caproni reassures him that even though his planes were used for evil, aviation itself is beautiful. Nahoko's spirit also comforts him, telling him to try to live his life to the fullest.