"Rei Rei" centers on a young girl named Rei, who lives in a dystopian future where humanity is on the brink of extinction due to a mysterious plague. The world is divided into isolated city-states governed by authoritarian regimes, each struggling to maintain control over dwindling resources. Rei, an orphan with no memory of her past, possesses a unique ability to manipulate time, a power that makes her a target for various factions vying for dominance.

The narrative begins with Rei living in the slums of Neo-Kyoto, a crumbling metropolis ruled by a militaristic council. She survives by scavenging and avoiding the attention of the authorities, who hunt down individuals with supernatural abilities. Her life takes a dramatic turn when she encounters Kaito, a rogue scientist who reveals that her powers are linked to a secret government project aimed at creating a weapon capable of reversing the effects of the plague. Kaito believes Rei is the key to humanity's survival and offers to help her uncover the truth about her origins.

As Rei and Kaito journey across the desolate landscape, they are pursued by the council's elite enforcers, led by Commander Akira, a ruthless officer determined to capture Rei at any cost. Along the way, Rei encounters other individuals with extraordinary abilities, including Yuna, a telekinetic rebel leader fighting against the oppressive regime, and Ren, a mysterious mercenary with his own agenda. These alliances and rivalries complicate Rei's mission, forcing her to confront the moral ambiguities of her powers and the consequences of her actions.

The plot delves into themes of survival, identity, and the ethical implications of wielding immense power. Rei's journey is marked by moments of introspection as she grapples with her role in a world teetering on the edge of collapse. The series builds toward a climactic confrontation in the ruins of Old Tokyo, where Rei must decide whether to use her abilities to save humanity or let the world succumb to its inevitable fate. The story concludes with an open-ended resolution, leaving room for interpretation regarding Rei's ultimate choice and its impact on the future.