In 1945, as World War II draws to a close, kamikaze pilot Koichi Shikishima makes an emergency landing with his Mitsubishi A6M Zero at a remote Japanese base on Odo Island. Despite the mechanics' thorough checks, they find no faults with the aircraft, leading lead mechanic Sosaku Tachibana to suspect that Shikishima is avoiding his military duties. While Shikishima reflects near the water, he observes striking deep-sea fish swimming close to the surface.
That same night, the camp is thrown into chaos when Godzilla, a gigantic creature familiar to the locals, attacks the garrison. Tachibana urges Shikishima to defend the base from his aircraft. However, paralyzed by fear, Shikishima is unable to pull the trigger and is rendered unconscious during the onslaught. Godzilla wreaks havoc, demolishing the base and rendering Shikishima's plane a total loss. When he regains consciousness the next day, he is devastated to learn that Tachibana is the only other survivor, and Tachibana's fury over Shikishima's inaction weighs heavily on him.
By December 1945, Shikishima returns to a devastated Tokyo, where he discovers his parents have perished in the bombing, leaving the city a smoldering ruin. Stricken with survivor's guilt, he finds solace in supporting Noriko Oishi, a woman who has also lost her parents, alongside an orphaned baby, Akiko (Sae Nagatani), whom Noriko vows to protect.
Their neighbor, Sumiko Ota, advises Shikishima that it is too late for heroics. However, after realizing an orphan girl is involved, she extends her help to Noriko, providing white rice to prepare gruel for little Akiko.
In March 1946, Shikishima secures a dangerous job aboard a minesweeper, tasked with clearing World War II naval mines—a venture laden with both financial reward and peril. Working alongside Kenji Noda, the crew faces the peril of American magnetic mines in their converted tugboats. Their captain, Yoji Akitsu, leads them in a mission fraught with uncertainty and danger. Over time, Shikishima begins to save enough to restore his home, while Noriko also finds work in the bustling Ginza district.
As fate would have it, in July 1946, Godzilla is mutated by U.S. nuclear testing, resurfacing at a time when tensions with the Soviet Union preclude any meaningful American assistance. Instead, a few old Imperial Navy vessels, authorized by General Douglas MacArthur, represent the only military support Japan receives. The government, afraid of sparking public panic, opts to keep the populace unaware of the impending doom.
By May 1947, the minesweeper crew goes out toward the Ogasawara Islands to engage with Godzilla. Witnessing the creature's monstrous size, their attempts to thwart Godzilla with mines and gunfire prove futile as it relentlessly pursues them. Desperate, they manage to damage Godzilla with a mine detonated in its mouth, but the creature's regenerative abilities are astonishing.
As they attempt to rally against the creature, their heavy cruiser, the Takao, meets a grim fate at Godzilla’s hands. Back in Tokyo, Shikishima confides in Noriko about his harrowing encounters with the beast. Shortly after, Godzilla invades Japan, targeting Ginza, where Noriko is working. Although she narrowly escapes the chaos, she is caught in the ensuing blast when Godzilla retaliates against tank fire, leading Shikishima to grieve a profound loss when she is presumed dead. The attack results in a staggering 30,000 casualties and the destruction of countless homes and buildings.
At a boiling point of frustration toward the government's indifference, Noda formulates a daring strategy to eliminate Godzilla. His plan involves luring the creature into Sagami Bay, where they intend to disrupt its buoyancy with Freon tanks. If that fails, strategically placed balloons would inflate beneath Godzilla to achieve explosive decompression. With a dedicated team of navy veterans, Shikishima recruits Tachibana, who restores a rusted prototype, the Kyushu J7W Shinden, and equips it for a final confrontation.
As Godzilla approaches, Shikishima bravely draws it into a trap set by destroyers. Despite the chaos and injuries that ensue, his plan takes a turning point when Shikishima sacrifices himself by crashing his plane into Godzilla's mouth. The explosion decimates Godzilla, triggering a triumphant moment for the crew as they rally together and celebrate Shikishima's courageous act.
Upon his dramatic return, Sumiko hands Shikishima a telegram that leads him to discover that Noriko survived the disaster, albeit bearing the scars of their shared tragedy. Yet, even as hope flickers, a piece of Godzilla’s flesh begins to regrow as it sinks beneath the waves, signaling the relentless cycle of destruction may not yet be over.
