30年前，未知的“侵略性外来生物”突然出现，世界曾一度濒临毁灭。人类与这些被称为“侵略种”的生物相互争夺生存空间。虽然目前人类的安全勉强得到了保障，但世界随时可能走向终结。人们在恐惧死亡与毁灭的同时，只能对危险和灾难视而不见，麻木地过着日常生活。在这样的世界里，联合国危险生物调查机构“EXCEEDS”为了抵御“侵略种”带来的危机与灾害，开始了行动。故事的开端位于远东的岛国“瑞穗”。一位在离岛上生活、以驱除“侵略种”为业的猎人少女——久濑椎名。她唯一的愿望就是与家中唯一的亲人妹妹刹那平静地生活下去。然而，降临在椎名身上的事件究竟是——？

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.

Takamachi Nanoha is a normal third-grader who feels a little useless and out-of-place with no purpose. Then one day, she saves a ferret, who turns out to be a mage from another planet who came to this planet to search for the jewel seeds. Nanoha agrees to help, but this task gets complicated when another girl arrives to steal them.

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".