Thirteen-year-old Nanoha Takamachi is no longer the same girl who once struggled under the weight of her own power. Following the events of the film continuity, specifically Reflection and Detonation, she has emerged brighter and more energetic, spending her days as a commissioned mage. A noticeable change is her newfound passion for aviation, often using any free time to attend aircraft exhibitions. This cheerful disposition delights her closest companions, Fate Testarossa Harlaown and Hayate Yagami, who see her embracing a more carefree youth than the one depicted in the original timeline.

The story centers on the trio’s activities within a newly formed organization called EXCEEDS. Founded and led by Hayate Yagami after she chose to leave the commander's course, EXCEEDS is an independent investigation agency operating directly under the Time-Space Administration Bureau. Its mission is to investigate global risks and prevent disasters, acting as a liaison with local security forces. The setting shifts primarily to the Darnaza Republic, a nation where sentient robots live alongside humans and a form of machine worship is prevalent. This world is haunted by the legacy of a brutal civil war that ended fifteen years ago, a conflict known as the Witch Hunt, which allegedly resulted in the complete extermination of a minority race known as the Witches.

The conflict reignites when military robots from the civil war begin to malfunction, suffering an awareness error that leads them to believe the war is still ongoing. They resume the hunt for their programmed "annihilation goal," the Witches, throwing the Darnaza Republic back into chaos. The Bureau tasks EXCEEDS with investigating the truth behind Darnaza's dark history. In the remote Mercure Village, a community of retired military robots, the team encounters Philippy Merquir, a young "robot doctor" who maintains the machines. Her father, Zeo, the village chief, is a former special forces soldier with a mysterious past connected to the legendary unit known as "Kishin ZED," and his body is heavily modified with cybernetics.

The narrative explores this new mission while redefining the relationships and futures of its main cast. The manga establishes a distinct timeline separate from the StrikerS continuity. Unlike the original series where Nanoha suffered severe injuries, here she is unharmed and thriving. Hayate has forsaken a traditional command path to build EXCEEDS from the ground up as an external organization, while Fate balances her duties as an officer with her personal life. As the investigation deepens, Nanoha, Fate, and Hayate confront a militaristic nation’s buried secrets and a conspiracy involving the supposed "annihilated" Witch race, all while navigating their lives as teenage officers in a world still healing from a devastating war.