The story begins in the year 2029, when the seabed along the Mediterranean coast suddenly sinks, causing oxygen to vanish abruptly. Following this event, various other elements that once existed begin to disappear one by one. With the absence of these natural elements, buildings, forests, animals, and all forms of life start to fade away as well. It is at this point that humanity truly realizes the importance of these "elements."
Sixty years later, the population has decreased to one-tenth of its original size. Investigations reveal that the missing elements have flowed to another Earth on the other side of the dimension, called "ネガアース" (Negāsu / Nega-Earth). Since only children under the age of 13 can reach "Nega-Earth," a group of these children, entrusted with the survival of the planet, is formed into an organization known as the "Element Hunters."