In 1945, near the end of World War II, kamikaze pilot Koichi Shikishima (Ryunosuke Kamiki) lands his Mitsubishi A6M Zero for repairs at the Japanese base on Odo Island. The mechanics cannot find anything wrong with the engine or the fuel-lines of the plane. The base itself is a small one and in the middle of nowhere and has a barely even landing surface, which means Shikishima was desperate to land there. Lead mechanic Sosaku Tachibana (Munetaka Aoki) deduces that Shikishima is feigning technical issues to flee from his duty. As Shikisima sits near the water, he sees deep sea fish on the surface. That night, Godzilla, a large dinosaur-like creature who is familiar to the locals, attacks the garrison. Tachibana tells Shikishima to fire at the monster from his plane. Shikisima manages to get into his plane, whose guns are pointing straight at Godzilla. But he panics, fails to shoot, and is knocked unconscious. Godzilla attacks the base and its soldiers and creates havoc. The small guns with the soldiers are not near enough to stop the Godzilla. Godzilla even destroys Shikisima's plane. When Shikisima awakes the following day, he finds Tachibana is the only other survivor, who is furious at him for failing to act.
In December 1945, Shikishima returns home to find his parents were killed in the bombing of Tokyo. The city itself was engulfed in flames and is now in ruins. Plagued by survivor's guilt, he begins supporting a woman, Noriko Oishi (Minami Hamabe), whose parents also died in the bombing, and an orphaned baby, Akiko (Sae Nagatani), whom Noriko rescued. Akiko's mother asked Noriko to take care of her. Sumiko is Shikisima's neighbor and tells him that it is too late to play the hero. When Sumiko finds that an orphan girl is involved, she helps Noriko and Shikishima to take care of it. She gives her white rice to Shikisima to make gruel for the baby.
In March 1946, Shikisima finds employment aboard a minesweeper tasked with disposing of naval mines from World War II. The job offers a lot of money, as the job is risky with a real possibility of death at any moment. The American magnetic mines are the most feared. Japan doesn't have specialized equipment to deal with the 60,000 mines and deploys 2 converted tugboats for the job. The wooden tugboats won't attract the magnetic mines. Noda works with Shikisima on the tugboats. The tugboats carry a cutter which cut the tethers of the mines to the ocean floor. When the mines float to the surface, they are exploded with a 13 mm gun. Yoji (Kuranosuke Sasaki) is their captain.
Slowly, Shikisima saves enough money to rebuild his home. Noriko finds a job in the Ginza. In July 1946, Godzilla is mutated and empowered by the United States' nuclear tests at Bikini Atoll; it sinks the submarine USS Redfish (which photographed the creature before being attacked and sunk. The parts of the submarine that came in contact with the creature had signs of radioactivity) and destroys several other ships (like the USS Lancaster) in route to Japan. Owing to tensions with the Soviet Union, the U.S. offers no help save for a few decommissioned Imperial Japanese Navy vessels approved by General Douglas MacArthur. The Japanese government, concerned about inducing panic, does not notify the public about the danger.
In May 1947, Shikishima and his minesweeper crew travel to the Ogasawara Islands and are tasked with stalling Godzilla's approach to Japan. The crew watches as the much bigger Godzilla takes out the 2nd tugboat with effortless ease. Shikishima's tugboat attacks Godzilla with their mines and guns but have little impact as Godzilla pursues them in the ocean. They release a mine into Godzilla's mouth and detonate it, causing significant damage, but it quickly regenerates.
Before Godzilla can destroy the tugboat, the heavy cruiser Takao (sent from the docks in Singapore) then engages Godzilla but is destroyed when the monster unleashes its heat ray. After returning to Tokyo, Shikishima opens up to Noriko about his encounters with Godzilla. Despite the gag order, Shikishima tells Noriko about his history with Godzilla. Days later, Godzilla makes landfall in Japan and attacks Ginza, where Noriko works. She narrowly survives the initial attack on the subway line and reunites with Shikishima (who had come to rescue her). Enraged by tank fire, Godzilla obliterates much of the district with its heat ray, killing tens of thousands. Noriko pushes Shikishima to safety but is caught in the blast and presumed dead. Devastated by the loss, Shikishima vows revenge. 30,000 people were killed in the attack. 20,000 homes and buildings were destroyed.
Frustrated by the government's inaction, one of the minesweeper's crew, former naval engineer Kenji Noda (Hidetaka Yoshioka), devises a plan to destroy Godzilla by luring it out to Sagami Bay (which is 1500 meters deep) before surrounding it with Freon tanks and rupturing them, lowering the water's buoyancy and sinking it, letting the resultant water pressure crush it. Should the plan fail, balloons will be inflated under Godzilla to force it back up, killing it through explosive decompression. Hotta (Miou Tanaka) is the head of the task-force working under Noda. This is a citizen led effort, as the Japanese armed forced do not exist, and the US will not support Japan, due to its continued cold war with Russia.
To enact his plan, Noda has recruited navy veterans to crew disarmed IJN destroyers (which were planned to be given away to the UN). Shikishima recruits Tachibana to repair a broken-down Kyushu J7W Shinden fighter. The Shinden is a prototype which was never deployed in the war but is the most maneuverable plane in Japan. Tachibana was required as the plane was rusting in a hangar and needed a crack mechanic to make it air-worthy. Tachibana loads the plane with 2 bombs and a machine gun. He plans to kill Godzilla in a suicide attack by flying into its mouth and detonating explosive charges on board. He leaves Akiko in the care of his neighbor Sumiko (Sakura Ando) before Godzilla resurfaces.
Noda gets reports of the Godzilla's movements towards Tokyo and calculates that Godzilla will reach Sagami Bay by 11 am the following day. But Godzilla is faster than anticipated and already crosses the shoreline. Shikishima attacks with his plane and lures Godzilla to the trap set by two destroyers. Sumiko receives a telegram intended for Shikishima. Godzilla survives the initial plunge and then breaks free before being forced back up, sustaining serious injuries from the resultant decompression-induced Barotrauma. With the help of a fleet of tugboats organized by Mizushima, another crew-mate from the minesweeper, the ships haul Godzilla to the surface. Enraged, Godzilla prepares to destroy all the vessels with its heat ray, but Shikishima crashes the plane into Godzilla's mouth and destroys its head, causing the energy of the heat ray to tear its body apart. The crew celebrates as Shikishima ejects before the explosion and parachutes to safety, using an ejection seat that Tachibana installed in the Shinden, imploring him to let go of his guilt and continue living.
Upon returning home, Sumiko gives Shikishima the telegram, which leads him to a hospital where he reunites with Noriko, who survived the destruction but has a black bruise creeping up her neck. Meanwhile, a chunk of Godzilla's flesh begins to regenerate as it sinks into the ocean.