The planet Eltria, having suffered severe desertification in the past, has all but been abandoned. Against her older sister's wishes, Kyrie Florian travels to Earth alongside her best friend, the AI Iris, in search of the key to their planet's regeneration. However, the only way to find it lies within the Tome of the Night Sky, leading them into conflict with Nanoha and her friends.

As the conflict that began in Magical Girl Lyrical Nanoha: Reflection continues to escalate, Nanoha and her allies soon find out the troubled history between Iris and Yuri, which is related to the tragedy of Eltoria's "Planet Reclamation Committee".