"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 trained to fight alongside their male partners, known as Limiters, who possess the ability to "freeze" the Nova and enhance the Pandoras' combat abilities. The story primarily unfolds at West Genetics Academy, a specialized institution where Pandoras and Limiters are trained.

The protagonist, Kazuya Aoi, is a Limiter who enrolls at West Genetics to follow in the footsteps of his late 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 resistance, Kazuya's unwavering support and determination gradually break through Satellizer's emotional barriers, forming a strong bond between them. Their partnership becomes central to the narrative as they face both external threats and internal conflicts within the academy.

The series explores the dynamics between Pandoras and Limiters, delving into themes of trust, loyalty, and the psychological toll of constant warfare. The Nova attacks serve as a recurring backdrop, escalating in intensity and complexity as the story progresses. The Pandoras' abilities, derived from their Stigmata—alien DNA integrated into their bodies—are a focal point, with each character exhibiting unique powers and limitations. The Limiters' role in enhancing these abilities through their Freezing techniques adds a strategic layer to the battles.

Key characters include Rana Linchen, a cheerful and determined Pandora who becomes a rival to Satellizer; Charles Bonaparte, a skilled Limiter with a mysterious past; and Gengo Aoi, Kazuya's grandfather and a high-ranking official overseeing the Pandora program. The series also introduces various factions and power struggles within West Genetics, highlighting the political and ethical dilemmas surrounding the use of Pandoras as weapons.

As the narrative unfolds, the origins of the Nova and the true purpose of the Pandora program are gradually revealed, raising questions about humanity's survival and the cost of genetic experimentation. The story balances intense combat sequences with character-driven moments, exploring the personal struggles and relationships of the Pandoras and Limiters as they navigate a world defined by conflict and sacrifice.