In Fujisawa, Sakuta Azusagawa is in his second year of high school. Blissful days with his girlfriend and upperclassman, Mai Sakurajima, are interrupted by the appearance of his first crush, Shoko Makinohara.
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..."
While sorting through a mess of books in the staff room, Ohana happens upon one of Denroku's log books from long ago. Within it, it recounts a story of Ohana's mom when she was the same age as her.