Sea levels have risen and a considerable amount of land had been lost due to global warming by 2039. As though in reaction, a strange fleet of mist-clad warships known as "the Fleet of Mist" materialized in every part of the ocean, assaulting human ships. Despite humanity's best efforts, they were completely destroyed by the Mist's overwhelming might. The Fleet of Mist blockaded all of humanity's trade channels, wrecked their political economy, and gradually weakened the human species. The submarine I-401 of the Fleet of Mist arrives in front of cadet Gunzo Chihaya seven years later. The sub's humanoid pilot, who should be their adversary, is instead giving her services to humanity.