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.

A floating space without gravity where an infinite number of lights shine in different colors: The "Box of Wisdom." Inside of this box, there are multiple worlds, multiple timelines, and there used to be many different people. This is where Dual and Dorothy were fighting with enemies called "Viruses." Worlds infected by viruses must be erased. That is the duty, the job of these girls. However, one day, Dual and Dorothy feel the presence of a new Virus. Arriving at the scene, they see a girl being attacked by Viruses. After saving the girl, the duo wait for her to awaken so they can ask who she is, where she came from, and where she is going. Finally, when the girl opened her eyes, she gave her name, Rimo, and whispered only one sentence... "I must return to the flower patch..."