In the year 2087, a secret organization known as the Space-Time Strategic Enforcement Unit operates from a dilapidated building. Its agents, called Fate Rewinders, are tasked with preventing catastrophic deaths across time and space. Each Rewinder possesses a prosthetic right eye called a Retry Eye, hidden beneath an eyepatch, which functions as a built-in time machine. By repeatedly rewinding time and using the knowledge gained from each failed attempt, they work to avert the demise of their designated targets. However, this power comes with a heavy cost; each rewind inflicts psychological damage and physical exhaustion, and a mission can become a war of attrition as a Rewinder must find the clear route to success before their body gives out. The organization also clashes with a notorious criminal syndicate known as the Clock Hands, who misuse time-travel technology for their own illicit ends.

The story follows Chrono, a kind-hearted and determined 14-year-old boy driven by an unwavering dedication to saving lives. After witnessing the unusual death of his beloved sister, Tokine, during an infamous unsolvable case designated Case 999, Chrono is inducted into the Enforcement Unit. He trains for several years under Shirai, a former Special Grade Rewinder who lost his own ability to rewind. Possessing a photographic memory, an analytical mind, and extraordinary mental fortitude, Chrono rises through the ranks with the aid of his sentient flying smartphone. His ultimate goal is to solve Case 999 and save his sister, a mission that brings him into frequent conflict with the Clock Hands, who seem determined to prevent him from succeeding.

Chrono is joined by a team of fellow Rewinders with their own unique abilities. Akaba is a cheerful and reckless 16-year-old katana-wielding fighter who was himself saved from a destined death by Shirai. Lemon is a 12-year-old combat gynoid with a calm, emotionless demeanor and immense firepower. Chainu is a meek and timid 18-year-old Rewinder with a mysterious past. As they tackle cases of increasing complexity, each Rewinder has the potential to awaken a unique Version Up ability, granting them limited command over an aspect of space-time itself. Chrono’s own Version Up, called Copy, allows him to summon an independent duplicate of himself from three minutes in the future. These allies work alongside Chrono as he confronts the psychological toll of his countless temporal loops and edges closer to the truth behind Case 999 and the Clock Hands.