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.