Patema is a plucky young girl from an underground civilization boasting an incredible network of tunnels. Inspired by a friend that mysteriously went missing, she is often reprimanded due to her constant excursions of these tunnels due to her royal status. After she enters what is known as the forbidden zone, she accidentally falls into a giant bottomless pit after being startled by a strange creature. Finding herself on the surface, a world literally turned upside down, she begins falling towards the sky only to be saved by Age, a discontented student of the totalitarian nation known as Aiga. The people of Aiga are taught to believe that Inverts, like Patema, are sinners that will be swallowed by the sky, but Age has resisted this propaganda and decides to protect his new friend. A chance meeting between two curious teenagers leads to an exploration of two unique worlds as they begin working together to unveil the secrets of their origins in Sakasama no Patema, a heart-warming film about overcoming differences in order to coexist.

Sophisticated, suave, sublime; all words which describe the exceedingly handsome and patently perfect Sakamoto. Though it is only his first day in high school, his attractiveness, intelligence, and charm already has the girls swooning and the guys fuming with jealousy. No one seems able to derail him, as all attempts at tripping him up are quickly foiled. His sangfroid is indomitable, his wits peerless. Will any of Sakamoto's classmates, or even teachers, be able to reach his level of excellence? Probably not, but they just might learn a thing or two trying...

Despite leading a peaceful life as the princess of a subterraneous colony, teenage Patema longs to escape her cramped industrial confines and experience someplace different. While satiating her curiosity by exploring a region known as the danger zone, she is startled by a cloaked figure and falls into the darkness of an abyss. Awakening with the sky below her feet and the ground hanging above, Patema finds herself clinging to a fence at the mercy of a seemingly reversed gravity. Although a nearby student named Age is able to rescue her, they are left wondering which of the two is actually upside down.

When Shoutarou Tatewaki first meets Sakurako Kujou, he knows his life will never be the same. Initially believing her to be responsible for a disappearance in the neighborhood, he later learns of her true talent: analyzing bone specimens. Sakurako has quite the collection of reconstructed animal bones, but she wishes she had more of the human variety, much to the chagrin of those around her. Soon, Shoutarou begins accompanying the eccentric osteologist on the many different unsolved cases she comes across—usually in the form of decomposing bodies. But with so many incidents happening around them, could there be a larger mystery at work in their lives? Sakurako-san no Ashimoto ni wa Shitai ga Umatteiru is a story of two unlikely partners, each showing in their own way that bones can tell how one died, but only people can tell how they lived.