"Empty Box and Zeroth Maria" is a psychological mystery manga series adapted from the light novel of the same name by Eiji Mikage. The story centers around Kazuki Hoshino, an ordinary high school student whose life takes a surreal turn when he encounters Aya Otonashi, a mysterious transfer student. Aya claims to have met Kazuki before, though he has no memory of her. She presents him with a strange object called the "Rejecting Marble," a device capable of resetting time by 24 hours. This marks the beginning of Kazuki's entanglement with a series of supernatural phenomena tied to mysterious artifacts known as "Boxes," each granting its user unique and often dangerous abilities.

The narrative unfolds through a series of interconnected arcs, each exploring the consequences of using these Boxes. Kazuki and Aya become central figures in a struggle involving other Box users, including Daiya Oomine, a manipulative and calculating individual who seeks to exploit the Boxes for his own ends. The story delves into themes of memory, identity, and the moral implications of altering reality. As Kazuki uncovers the truth about the Boxes and their origins, he is forced to confront the ethical dilemmas posed by their power and the personal sacrifices required to resolve the conflicts they create.

Aya Otonashi, the enigmatic heroine, plays a pivotal role in the story. Her connection to the Boxes and her past are gradually revealed, shedding light on her motivations and the deeper mysteries surrounding the artifacts. The relationship between Kazuki and Aya evolves as they navigate the challenges posed by the Boxes, blending elements of trust, betrayal, and emotional vulnerability. Supporting characters, such as Kazuki's childhood friend Haruaki Usui and the morally ambiguous Daiya, add complexity to the narrative, each contributing to the overarching tension and philosophical undertones of the series.

The plot is structured around a series of escalating conflicts, with each arc introducing new Boxes and their users, while gradually unraveling the overarching mystery of the "Zeroth Maria," a legendary Box said to possess unparalleled power. The story's pacing balances intense psychological drama with moments of introspection, creating a narrative that is both intellectually engaging and emotionally resonant. The series concludes with a resolution that ties together the various threads of the story, offering a satisfying conclusion to the characters' journeys and the mysteries of the Boxes.