Gunjo Academy serves as a center for students with high scores on an adaptation exam. The facility isolates these individuals from society due to their low adaptability potential. Following a disappointing summer break spent alongside other school club members, Kurosu Taichi and some of his peers return to the city only to discover that all living beings except for themselves have vanished. In order to verify the condition of the outside world, Taichi enlists the help of Misato, president of the broadcasting club, as she attempts to establish a contact antenna with any potential survivors.