The film revolves around a mysterious girl named Éclair who appears before Fairy Tail, the world’s most notorious wizard’s guild. She lost all of her memories, except for the imperative that she must deliver two Phoenix Stones somewhere. The stones may spell the collapse of the magical world, and Natsu, Lucy, and the rest of the Fairy Tail guild are caught up in the intrigue.

In the story, the seasons have changed and it will soon be the second spring. Tatsuya and Miyuki have finished their first year at First Magic High School and are on their spring break. The two go to their villa on the Ogasawara Island archipelago. After only a small moment of peace a lone young woman named Kokoa appears before them. She has abandoned the Naval base and she tells Tatsuya her one wish.