Years have passed since the King of the Monsters, Godzilla, emerged to ravage the Shinjuku district of Tokyo before vanishing without a trace. In the wake of this catastrophe, a young girl named Miyu Kaido loses her family and is profoundly marked by the creature's awesome and terrifying power. As she grows into a brilliant but deeply eccentric teenager, humanity has achieved a new milestone: the technological capability to travel into outer space. This era of hope is short-lived, however, as a mysterious and colossal unidentified lifeform descents upon Earth, presenting a threat unlike any previously encountered.

This new enemy is Volga, a space kaiju of immense power and strange design, commanded by an alien race known as the Nebula. With the Earth's military forces struggling against Volga’s devastating heat rays and crippling electromagnetic pulses, the situation seems hopeless. But as the alien monster lays waste to a Japanese city, a familiar roar echoes from the sea. Sensing an intrusion on its territory, Godzilla emerges to confront this cosmic rival, initiating a brutal duel between the King of the Monsters and an extraterrestrial foe.

The story is centered on Miyu Kaido, now a gigantology researcher whose obsession with Godzilla borders on the pathological. Unlike those who see only hatred for the beast that ruined her life, Miyu harbors a complex and unsettling fascination, even finding a twisted sense of beauty in Godzilla's destructive power. Her genius-level intellect makes her a key strategic consultant for the military, where she works alongside Second Lieutenant Shinya Osaki, a pilot who bears his own scars and grievances against Godzilla. Together, they represent humanity's fragile hope: one driven by analytical obsession, the other by a desire for vengeance.

After witnessing Godzilla defeat Volga, Miyu comes to a realization about her own psyche and proposes a radical plan. To combat the growing threat of space monsters, she suggests humanity should capture Godzilla, transport it into the cosmos, and use it as a living weapon. This leads to Operation Godzilla Capture, an ambitious and dangerous scheme to lure the monster into a colossal space-faring vessel named the Gotengo. The operation, however, goes disastrously wrong when Godzilla fights back, leading to a desperate struggle for control and survival.

The narrative unfolds in distinct arcs, beginning with the "Godzilla vs. Volga" arc, which establishes the cosmic setting and the primary conflict. This is followed by the "Godzilla Capture Operation" arc, where the focus shifts to the perilous human plan to harness the monster. Throughout these arcs, the series maintains a relentless focus on monster action, featuring dynamic battles and showcasing Godzilla's signature atomic breath alongside its formidable physical prowess. The human drama serves to frame the kaiju conflict, exploring the psychological impact of living in a world dominated by giant monsters and setting the stage for an interstellar journey where Earth's greatest disaster may become its only hope against the void of space.