The film opens with a glimpse of the Asahi Shimbun's special expedition to the wreckage of the Yamato in 1999. The story then transitions to the present day on April 6, 2005, where a woman named Makiko Uchida is visiting the Yamato Museum in Kure, Hiroshima. She is on a quest to find a boat that will take her to the site where the Yamato sank, aiming to pay tribute to the crew on the sixtieth anniversary of the ship's final battle. During her search, she encounters Katsumi Kamio, a survivor of the Yamato who has since become a fisherman. Upon learning that Makiko is the adopted daughter of Petty Officer First Class Mamoru Uchida, who was a cherished crew member and close friend he thought went down with the ship, he agrees to take her. Despite being confirmed deceased a year ago, Kamio’s hope that Uchida survived reignites.
As they journey to the location aboard Kamio’s fishing boat, accompanied by his teenage apprentice Atsushi, the narrative shifts back and forth between their present voyage and Kamio’s vivid memories of his time serving as an air defense crewman on the Yamato during World War II.
In the spring of 1944, Kamio and a group of young cadets, most of whom are mere teenagers, are assigned to the Yamato. They endure strict training under the watchful eyes of Petty Officers Uchida, Shohachi Moriwaki (played by Takashi Sorimachi), and Karaki, who have all been part of the crew since its commissioning in 1941. The situation escalates in October 1944, when the Yamato sets sail with a large Japanese fleet for a confrontation against American forces in the Battle of Leyte Gulf. The ship endures significant hits during the battle, resulting in the loss and injury of numerous crew members. After sustaining these damages, the Yamato returns to Japan for repairs while Uchida recuperates in a hospital after losing his left eye during the combat.
As the story unfolds into March 1945, whispers of an impending mission against an expected Okinawa invasion circulate among the crew, leading to a brief period of shore leave. During this time, Kamio visits his home, only to find that his mother has perished while shielding his girlfriend, Taeko Nozaki (played by Yu Aoi), during an air raid in Kure. Taeko confesses her love for him, giving him a special amulet for protection just as he prepares to head to Okinawa.
Taking advantage of his shore leave, Uchida sneaks away from the hospital to rejoin the crew. Meanwhile, they receive a briefing from Vice-Admiral Ryūnosuke Kusaka about Operation Ten-Go which will likely turn into a suicide mission. With no air cover, the Japanese forces are at great risk of Allied attacks, making their chances of reaching Okinawa exceedingly slim. Tensions flare amongst the crew as some deem the mission ill-fated, but they are ultimately rallied by an officer, emphasizing that the Yamato—being Japan's last active battleship—must make every effort to protect the homeland.
On the fateful morning of April 7, the Yamato, along with its escorts, initializes battle stations as Task Force 58 detects them and deploys strike planes to intercept. As U.S. aircrafts storm in, the crew springs into action with their anti-aircraft defenses. Yet, the overwhelming numbers of enemy planes prove too much, leading to severe damage on the Yamato from bombings and torpedoes. Kamio, Uchida, and Moriwaki strive to operate a portside anti-aircraft battery, even as they witness many crew members, including Karaki, fall in battle. When it becomes clear that the ship is sinking, orders are given to abandon ship by Vice-Admiral Seiichi Itō and Captain Kōsaku Aruga. Though they choose to remain on board, Uchida and Moriwaki force Kamio to abandon his post despite his reluctant desire to stay with them to the end. As the ship begins to capsize and ultimately explodes after its aft magazine detonates, Kamio finds himself fighting for survival.
Following the tragic sinking, the remaining vessels attempt to rescue survivors, but Kamio is unable to save his friend Tetsuya Nishi despite having promised his mother to keep watch over him. In a heart-wrenching moment, Moriwaki ties Kamio to be hoisted aboard a rescue boat, swimming away from safety to drown himself.
The narrative fast-forwards to the present, where an older Kamio suffers a heart attack but is revived by Makiko and Atsushi. He shares the haunting memories from the war's final days, conveying the sorrow of not being able to protect those he loved, including Taeko, who succumbed to radiation poisoning following the atomic bombing of Hiroshima while she was forced to work at a munitions plant. Despite this tragedy, she had the chance to see him one last time before her death, referring to his boat as Asukamaru.
As they reach the coordinates of the sinking the next day, a poignant ceremony takes place. Makiko scatters Uchida’s ashes while Kamio presents her with a dagger that Uchida entrusted him with during the battle—the dagger that was an invaluable gift from Admiral Isoroku Yamamoto when the Yamato served as his flagship. The three individuals reflect on their shared history and experiences before making their way back to Japan following the respectful memorial.
In the end credits, viewers see Makiko placing flowers at a dedicated memorial for all those who perished in that fateful encounter.
