"Freezing" is set in a future where Earth is under constant threat from interdimensional beings known as Nova. To combat this threat, genetically enhanced female warriors called Pandoras are paired with male partners known as Limiters, who use special abilities called Freezing to restrict the Nova's movements. The story primarily unfolds within the confines of West Genetics Academy, a training institution for Pandoras and Limiters.

The protagonist, Kazuya Aoi, is a Limiter who enrolls at West Genetics to follow in the footsteps of his late sister, Kazuha Aoi, a legendary Pandora. Kazuya forms a partnership with Satellizer el Bridget, a highly skilled but socially isolated Pandora known as the "Untouchable Queen" due to her aversion to physical contact. Despite her formidable abilities, Satellizer struggles with emotional trauma and a troubled past, which Kazuya gradually helps her overcome through their growing bond.

The narrative explores the dynamics between Pandoras and Limiters, emphasizing the importance of trust and synchronization in battle. As Kazuya and Satellizer face various challenges, including rivalries with other Pandoras and Limiters, they also confront the larger threat posed by the Nova. The series delves into the personal struggles of its characters, including themes of loss, identity, and the psychological toll of combat.

Key supporting characters include Rana Linchen, a determined Pandora who develops feelings for Kazuya, and Charles Bonaparte, a Limiter with a strategic mind who becomes a close ally. The story also introduces antagonists such as Gengo Aoi, Kazuya's grandfather and the head of West Genetics, whose morally ambiguous actions and hidden agendas add complexity to the plot.

As the series progresses, the stakes escalate with the emergence of stronger Nova and internal conflicts within West Genetics. The narrative balances intense action sequences with character-driven moments, exploring the relationships and motivations of its diverse cast. "Freezing" combines elements of science fiction, romance, and drama, creating a multifaceted story that examines both the personal and global consequences of humanity's fight for survival.