Original story based on Yoshitomi Akihito's Blue Drop manga. In 1995, all 800 inhabitants of the isolated Kamikakushi Island vanished in one night, all but a single girl who lost her memory. The cause of the disappearances was never identified. Four years later, that girl, Mari, transfers to the girl's dormitory school, Kaihou Gakuen, leaving behind her grandmother, who had been her guardian ever since the incident. There, she meets Hagino. Hagino is the school idol and completes her student council responsibilities flawlessly. The moment she touches Mari's hand, however, Hagino freaks out, straddling atop Mari, hands around her throat. Mari is afraid of and angry at Hagino, who pretends as if nothing had happened while in front of other students, but at the same time, somehow, she is attracted to Hagino. As it turns out, Hagino is actually an alien who was sent to Earth in order to reconnoitre prior to an invasion. The event on Kamikakushi Island occurred when the 200-member crew of a battleship, the Blue, whose captain was Hagino and the island's inhabitants killed each other. The Blue was seriously damaged and hidden. Hagino had since blended into human society and continued her reconnaissance. Enduring her school life, fighting with fellow students, Mari begins to come out of her shell. Hagino has been living a double life, but her encounter with Mari makes her see human beings in a different light, and gradually she begins to have doubts about her mission. While the impeding invasion and war draw ever closer, the girls begin to understand each other.