A force known as Astral power permeates throughout the world, wielded by astral mages. Fearing its destructive power, the Empire persecutes those who show their abilities. The tormented mages then founded the Nebulis Sovereignty to flee from their oppressors. Since then, the two nations have been in bitter conflict, the war still going strong for more than a century. After committing the great crime of freeing an imprisoned witch, the talented knight Iska is sentenced to prison. A year later, the Empire leadership suddenly decides to set him free, with the condition that he hunts down a fearsome mage known as the Ice Calamity Witch. Hoping to end the war, Iska agrees. Coincidentally, the Ice Calamity Witch herself, Aliceliese Alice Lou Nebulis XI, also wishes for peace and is willing to do everything she can to bring down the Empire. As Iska and Alice both yearn for a crusade that will turn the world into one without struggle, woe, or pain, the strings of fate tie them ever closer together, creating a bond that goes beyond something fabricated by mere coincidence.

Keitaro Urashima promised a girl when he was young that they would meet up again at Tokyo University in the future. Sadly, in the National Practice Exam, Keitaro ranked 27th from the bottom. Knowing his grandmother owned a hotel, Keitaro intended to stay there while continuing his studies for Tokyo U, only to find out the hotel had long been transformed into an all-girls dormitory. Through an odd twist of fate, Keitaro eventually became the manager of the dorm, beginning his life of living with five other girls.

The king of Natra has fallen ill, leaving the only hope for his kingdom to his son, Prince Wein Salema Arbalest. Known to be capable and wise, he is the perfect candidate to become the prince regent. However, if the prince has anything to say about the matter, he would rather sell off the Kingdom of Natra to the highest bidder! Since he wields the authority of the throne, no one can stop Wein from auctioning off the country and using the profits to retire in comfort. All he needs to do is raise the value of the small kingdom to maximize his gains. But whether Wein's grand plan will succeed remains to be seen, as his wit often surpasses even his own expectations—much to the benefit of the oblivious citizens of Natra.

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.