"Freezing" is set in a future where Earth is under constant threat from interdimensional beings known as Nova. To combat this, genetically enhanced female warriors called Pandoras, equipped with special weapons and abilities, are trained to fight alongside their male partners, known as Limiters, who provide support by using a power called Freezing to immobilize the Nova. The story primarily unfolds at West Genetics Academy, a specialized institution where Pandoras and Limiters are trained.

The protagonist, Kazuya Aoi, transfers to West Genetics to become a Limiter following the death of his older sister, a legendary Pandora. Kazuya is paired with Satellizer el Bridget, a highly skilled but socially isolated Pandora known as the "Untouchable Queen" due to her refusal to accept a Limiter. Despite her initial cold demeanor, Satellizer gradually forms a bond with Kazuya, who is determined to support her both in battle and emotionally. Their relationship becomes central to the narrative, as Kazuya’s unwavering loyalty helps Satellizer confront her traumatic past and overcome her fears.

The series explores the dynamics between Pandoras and Limiters, emphasizing the importance of trust and partnership in combat. It also delves into the competitive and often harsh environment of West Genetics, where students are ranked based on their abilities and must prove themselves in simulated battles and real-world missions. Key characters include Rana Linchen, a fiery and determined Pandora who develops a rivalry with Satellizer, and Charles Bonaparte, a skilled Limiter who becomes a close ally to Kazuya.

As the story progresses, the threat of the Nova intensifies, leading to large-scale battles that test the limits of the Pandoras and Limiters. The series also introduces deeper mysteries surrounding the Nova, their origins, and the true purpose of the Pandora program. Themes of sacrifice, resilience, and the bonds forged in adversity are woven throughout the narrative, as the characters face both external enemies and internal struggles. "Freezing" balances action-packed combat with character-driven drama, creating a story that is both engaging and emotionally resonant.