In the final days of World War II, a young kamikaze pilot named Koichi Shikishima lands his fighter plane on Odo Island, falsely reporting a mechanical failure to avoid his suicide mission. There, the base's lead mechanic, Sosaku Tachibana, quickly realizes the deception but is given no time to dwell on it when a massive, dinosaur-like creature the locals call Godzilla emerges from the sea and attacks. Shikishima, frozen with fear, fails to fire his plane's guns at the monster, and he is the only person, aside from Tachibana, to survive the onslaught.

The war ends shortly after, and Shikishima returns to a devastated, bombed-out Tokyo to find his parents dead and his home destroyed. Haunted by survivor's guilt and shunned by a neighbor who despises him for his cowardice, he struggles to find meaning in a nation reduced to zero. He soon encounters a determined young woman named Noriko Oishi, who is caring for an orphaned baby, Akiko. She essentially invites herself and the child into his ruined home, forming an unconventional family unit. To support them, Shikishima takes a dangerous, high-paying job as a minesweeper on a small wooden boat, working alongside a veteran crew including Captain Yoji Akitsu, the brilliant former weapons developer Kenji Noda, and a young rookie, Shiro Mizushima.

Unbeknownst to the public, Godzilla has been mutated and supercharged by American nuclear tests in the Pacific, growing to immense size and gaining the terrifying power of an atomic breath that can level a city with a single blast. As Godzilla begins attacking ships and advancing toward the Japanese mainland, the government proves paralyzed, refusing to act for fear of provoking the Soviet Union. Shikishima's minesweeper crew has a terrifying encounter with the monster at sea, where they witness its horrific regenerative abilities, capable of healing wounds almost instantly. The creature follows them to the coast and makes landfall in the Ginza district of Tokyo, unleashing its nuclear breath in a catastrophe that mirrors the atomic bombings. During the attack, Noriko sacrifices herself to push Shikishima to safety, seemingly dying in the blast.

Devastated and determined to end his war, Shikishima volunteers for a desperate, citizen-led plan devised by Kenji Noda. The strategy involves luring Godzilla into the deep waters of Sagami Bay, using steel cables to trap it, and rapidly decompressing its body by surrounding it with freon tanks and explosive balloons. Shikishima is tasked with the final, suicidal step: flying his old fighter plane, loaded with bombs, directly into Godzilla's mouth to destroy its head from the inside, a kamikaze act of atonement. As the complex plan unfolds and seems to fail, Shikishima launches his attack. At the last possible moment, he ejects from the plane—thanks to an ejector seat secretly installed by Tachibana, who had urged him to "live"—while the aircraft detonates, tearing Godzilla apart.

In the aftermath, Shikishima reunites with his adoptive daughter, Akiko, and receives a miraculous telegram: Noriko is alive, though injured and recovering in a hospital. As they embrace, a dark, bruise-like mark of Godzilla cells is visible growing on Noriko's neck, and on the sea floor, the remains of Godzilla's flesh begin to regenerate, promising a future return.