"Calabi-Yau no Sukima" is a science fiction anime series that explores themes of parallel universes, quantum mechanics, and human relationships. The narrative centers on two main characters, Ryou and Aya, who are childhood friends and researchers working on a groundbreaking project involving dimensional physics. Their work focuses on the theoretical concept of Calabi-Yau manifolds, which are hypothesized to exist in higher-dimensional space and could potentially allow for the traversal between parallel universes.

The story begins with Ryou and Aya successfully creating a device capable of detecting and interacting with these higher-dimensional spaces. However, their experiments inadvertently open a rift to a parallel universe, leading to unforeseen consequences. As they delve deeper into their research, they discover that their actions have caused a destabilization in the fabric of reality, creating anomalies that threaten both their world and the alternate universe they have connected to.

Throughout the series, Ryou and Aya grapple with the ethical implications of their work, as well as the personal toll it takes on their relationship. The narrative explores their struggles to reconcile their scientific ambitions with the potential dangers posed by their discoveries. As the anomalies grow more severe, they are forced to confront the possibility that their actions could lead to catastrophic outcomes for both universes.

Supporting characters include fellow researchers and government officials who become involved in the project, each bringing their own perspectives and motivations. The series also introduces alternate versions of the main characters from the parallel universe, adding layers of complexity to the story as the characters navigate their interactions with their counterparts.

The plot is driven by a combination of scientific intrigue and emotional tension, as Ryou and Aya work to understand the nature of the Calabi-Yau manifolds and find a way to stabilize the rifts they have created. The series balances technical explanations of theoretical physics with character-driven drama, creating a narrative that is both intellectually engaging and emotionally resonant. The resolution of the story hinges on the characters' ability to make difficult choices that will determine the fate of their worlds.