The dying planet of Eltria is the only home of Kyrie Florian, her older sister Amitie, and her parents, who are scientists researching ways to save it. Unfortunately, the Florians must leave the planet behind to seek medical care for their father, who has contracted a lethal illness.

Even with treatment, the survival rate of Kyrie's father is minuscule. Refusing to give up on her father and Eltria, Kyrie goes against the wishes of her sister and runs away from home to the peaceful planet of Earth in search of a solution. There, Kyrie and her childhood friend, Iris, pursue Earth's magical protectors—Nanoha Takamachi, Fate Testarossa, and Hayate Yagami.

Nanoha and her companions possess the key to fulfilling Kyrie's objective, and the young girl must do whatever it takes to obtain it. However, it proves difficult for Kyrie, as the protectors do not easily yield to her provocation. Furthermore, Amitie soon arrives on Earth to stop her younger sister's reckless actions and bring her back home, further complicating the already delicate situation.