In the film’s introduction, an experiment in the near future to attempt harness of the Earth’s gravity for energy results in the devastation as much of the surface with nearly everyone and everything is thrown into a reverse gravity field and sent flying from the Earth.
Unknown years pass, Patema is a respected teenage girl lives in a society that resides underground. Inspired by her friend Lagos, who had left some years before, she explores the tunnels. One day, while looking at a large seemingly bottomless hole, she is scared by a figure that appears to walk on the ceiling, and she falls into the pit. Age is a teenage boy, living in the totalitarian nation of Aiga, founded to protect its citizens from “danger zones” that were created by the earlier experiment. He has been traumatized for some time after watching his father suffer a fatal accident while attempting to demonstrate a flying machine, and desires to continue his father’s dream. While daydreaming at night near a fence surrounding Aiga, he hears a noise nearby to find Patema there, whose gravity is inverted from his. After helping her safely to the ground to avoid having her fly off into the sky, he takes her to a nearby shed, where they learn about each other’s worlds. Age discovers that by the two gripping each other, they can reduce the rate at which he falls, and he suggests using this to help return Patema to her people.
Aiga’s leader Izamura, who sees the failed experiment and the “Inverts” (those who suffer from inverted gravity) as a sin, wants to eliminate them. When he discovers Patema’s presence via numerous security cameras, he has his troops capture Patema and Age. Age is scolded and reprimanded, while Izamura takes Patema to his giant governing tower, threatening to release her into the sky, and shows her that he had previously captured another Invert, Lagos, who has long since died. He imprisons her in the top floor, with only a plate of glass between her and the sky should she “fall”.
Age returns to the place where he met Patema, and is surprised to find Porta, one of Patema’s friends, coming up to find her. Age goes with Porta to the underground tunnels, finding himself an Invert among those people. They, along with the society’s Elder, devise a plan to free Patema. Age and Porta work together, using the same means of each other’s weights to offset gravity, to sneak into the tower by going through its abandoned basement. Age enters the top floor alone and frees Patema, but Izamura and numerous forces soon arrive, chasing the two to the roof. Izamura grabs Patema and orders his right-hand man, Jaku, to shoot Age. Jaku hesitates, then Patema instead jumps off Izamura, grabs Age, and the two float off into the sky because Patema is tied with an inverted weight to her leg, shocking everyone watching, including Porta. Izamura then orders to have Age’s death reported as an accident.
Age and Patema continue to fly up, but as they make it through the clouds, they find that the “sky” appears to be a mechanical creation that projects the appearance of stars for Aiga. They discover Age’s father’s flying machine having “fallen” to the sky, and Age reads his father’s notes, learning that he had met Lagos, and together they worked to create the flying machine. After spending the night, they find the mechanical sky is now lit like the sun, and they release the weights that had given the craft buoyancy, letting it fall steadily back to Aiga. Meanwhile, Jaku is suspicious about Izamura’s orders, and discovers that Izamura had Age’s father killed, specifically to prevent anyone from discovering how small Aiga is. As Izamura finds Jaku’s snooping, they spot the flying machine falling back to the ground. Kaho, Age’s classmate, who believed in him and doubts that his “death” was accidental, she and everyone else witness the flying machine, and Izamura orders his troops to capture it.
Age and Patema jump from the flying craft, their negating weight allowing them to drift into the large hole that Patema originally fell out of. The underground residents glad to see the two alive. However, Izamura and Jaku follow in the flying craft, which ends up falling to the floor of the large shaft. Ignoring Izamura, Jaku turns to help the troops from falling. Izamura shoots and wounds Age, and then attempts to kill Patema when Porta arrives, knocking away the gun and a knife before he loses his grip and falls up the shaft. The floor of the shaft shatters, revealing sky below it. Izamura grabs Patema as he falls into the sky, followed by Age, and they see thousands of ruins of buildings around and truly open sky, including a ring of debris about the Moon; it is revealed that it is Aiga and its citizens are those that actually survived the catastrophic incident despite their gravity being inverted, and were living in an artificial world and sky underground which supported this inverted gravity.
Izamura loses his grip on Patema when the remains of the flying craft fall onto him, sending him into the sky to his demise. Age is able to jump and grab onto Patema, and Jaku and the Elder, who had saved Porta, quickly secure the two from falling either way. Age wakes to discover the true situation, while the Elder read the notes about his son Lagos, and Jaku agree that their worlds should work together now the truth is known. Like how Age had helped Patema, Patema holds onto Age while they explore the surface.