In the Four Islands Archipelago, people can use Grav-Shoes to fly around! This is the story of Asuka Kurashina, a transfer student that arrives at Kunahama Academy from outside the Four Islands. After seeing the ability of wearers to soar in the sky, she quickly develops an interest in flying with the Grav-Shoes and also joins the school's FC (Flying Circus) club to further her passion.

Shinichi Izumi is a normal high school boy whose right hand has become infected with an alien parasite that names itself "Migi" ("right"). Migi is the first parasite to develop a symbiotic relationship with its host, as he and Shinichi slowly develop a grudging friendship. Migi isn't the only Parasite on earth, however, and as cases of Parasites killing humans begin to emerge, humans seek to kill off Parasites. Shinichi and Migi find themselves caught in between these two sides of the struggle over planet earth.