Takamachi Nanoha is a normal fourth-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 jewl seeds. Nanoha agrees to help, but this task gets complicated when another girl arrives to steal them.

A pair of researchers remain on their dying planet of Eltria with their two daughters, Amitie and Kirie, in hopes of finding a way to revive the planet, but it was no use. Against her older sister's wishes, Kirie sets off with her childhood friend Iris to seek help from a distant alternate world. They arrive in Japan on Earth to search for the key to their planet's regeneration.

The film will delve into the history between Iris and Yuri, and the tragedy of Eltoria's "Planet Reclamation Committee."