In the year 2067, a scientific experiment aimed at harnessing energy from Earth's gravity goes horribly wrong, leading to a catastrophic reversal of gravity, causing most of humanity and objects to drift away from the planet.
Fast forward to a post-apocalyptic future, where Patema, a courageous young girl, resides in an underground community that instills strict regulations to protect its inhabitants from the surrounding "danger zones." This tightly controlled society is forever altered when Patema, emboldened by the mysterious disappearance of her friend Lagos, ventures into the dark tunnels. During her exploration, she encounters a surprising figure walking along the ceiling, which sends her tumbling down into the abyss below.
Patema's fall lands her outside the confines of her underground home, in a peculiar region known as Aiga. Here, she meets Eiji, another teenager whose gravity is oriented differently than her own. After safely bringing Patema to the ground, Eiji introduces her to his world, where he recounts the tale of his father, who once fell from a flying craft during a demonstration—an act that has been construed by the government as part of the phenomenon of the "Inverts."
However, their newfound connection is soon jeopardized when Aiga's tyrannical leader, Izamura, learns of Patema's presence and dispatches his forces to capture her. Eiji realizes that holding onto Patema allows him to defy gravity, slowing his descent and helping them dodge Izamura's troops. Despite their best efforts, they are ultimately captured, and Eiji is reprimanded for his actions. Meanwhile, Izamura imprisons Patema at the Control Tower, threatening to release her into the open sky, and reveals that he has captured Lagos, who has sadly passed away.
In a twist of fate, Eiji returns to the fence where he unexpectedly finds Porta, one of Patema's friends, who drags him reluctantly into the underground society. Together with the community's Elder, they formulate a daring plan to rescue Patema. Teaming up with Porta, Eiji uses their contrasting weights to infiltrate the tower through its abandoned basement. Eiji bravely ascends alone to the top floor and liberates Patema, but their freedom is short-lived as Izamura and his men soon chase them to the rooftop. In a desperate moment, Patema leaps from Izamura's grasp to rescue Eiji, and together they float skyward, defying the odds.
As they ascend, the unconscious duo awakens to witness a startling revelation: the so-called "sky" is merely a mechanical ceiling that manufactures Aiga's artificial atmosphere and projects faux stars. Here, they stumble upon Eiji's father's flying machine and discover notes revealing that both he and Lagos had a hand in its creation. Amidst their thrilling adventure, Eiji and Patema share a heartfelt declaration of love, freeing the inverted weights keeping the craft grounded, allowing it to ascend back towards Aiga.
Meanwhile, Izamura's right-hand man, Jaku, grows suspicious of his leader’s motives. He uncovers the shocking truth that Izamura orchestrated the death of Eiji's father and imprisoned Lagos, seeking to maintain control and hide the reality of their small world. As Izamura confronts Jaku, they observe the return of the flying machine, prompting him to order the capture of Eiji and Patema. Outside, Eiji's classmates, including Kaho, notice the craft and question the legitimacy of his supposed "accident."
In a dramatic turn of events, Eiji and Patema leap from the craft as it descends, plummeting into the very shaft leading back to Patema's underground society. The jubilant Inverts celebrate their return, but their joy is short-lived as Izamura and Jaku pursue them. A fierce confrontation ensues, resulting in Eiji getting injured while trying to shield Patema. As the battle intensifies, Porta heroically knocks the gun away from Izamura, who resorts to a knife to eliminate Patema. Yet, just as he strikes, the floor beneath them collapses, revealing the desolate surface of the Earth, scattered with the remnants of civilization and an open sky above, exposing Aiga’s shocking truth: they are the last survivors of a failed experiment living underground.
As the chaos unfolds, Izamura desperately clings to Patema but loses his grip when the damaged craft collides with him, sending him high into the atmosphere. In a heroic act, Eiji leaps to catch Patema, and with the help of Jaku and the Elder, they secure their survival. Eiji eventually awakens to the haunting beauty of the surface world, while the Elder reads through Lagos's notes, enlightening them about their shared history. With the truth unveiled, Eiji, Porta, and Jaku agree to unite their worlds, while Patema and Eiji embrace one another, ready to face the dawn of a new era.
