In 2065, Earth is in the middle of a war with extra-dimensional aliens called Nova. The military develops and trains Pandoras, girls who are able to use special genetic tissue called Stigmata to manifest superhuman fighting skills and weapons. Supporting the Pandoras are male partners called Limiters, who use special "freezing" powers to limit their opponent's mobility.

One of these limiters is you, whose late sister was a Pandora. While attending West Genetics Academy in Japan, you met Satellizer el Bridget, a powerful Pandora, nicknamed the Untouchable Queen, for her ruthless personality and her intense aphephobia. Despite warnings from your schoolmates to keep away from Satellizer, you surprisingly befriends her. After helping her through several fights against school rivals of varying ranks and classes, Satellizer partnered up with you by her choice, although she soon encounters a rival in romance named Rana Linchen, who thinks you’re is her soulmate.