Decades into the future, humanity is under siege by an alien race known as the Novas. These inhuman beings leave devastation in their wake whenever they appear, with the efforts to stave them off becoming known as Nova Clashes. Young women known as "Pandoras" and young men known as "Limiters" are implanted with stigmata to give them superhuman powers and are trained in military academies, where they must learn to work together if humanity is to have a chance of surviving. Freezing tells the story of Kazuya Aoi as he sets out for his first day at the West Genetics military academy, right when a battle royale is being undertaken by the Pandoras. It is here that he mistakes Satellizer el Bridget—a powerful Pandora known as the "Untouchable Queen"—as his deceased sister and embraces her. Though he costs her the match, she finds that his touch doesn't drive her away and decides to take him as her Limiter. The only question is whether or not their partnership can survive the machinations of their upperclassmen and the impending battle with the Novas…Set in a slightly futuristic world where Earth has been invaded and is at war with aliens from another dimension called the Nova, the story follows the adventures of a Japanese boy named Kazuya Aoi who enrolls for training at a special school for genetically modified girls called Pandoras who battle the aliens, and their male partners, called Limiters, who use a special power called "freezing" to limit their opponent's mobility. The protagonist makes the acquaintance of an unusual older girl named Satellizer el Bridget who appears to be the most powerful Pandora in her class, but has not yet chosen a male partner to be her Limiter, and in spite of the warnings of all his friends, he decides to be her Limiter.