Humanity finds itself in a struggle when the sea level begins to rise to an unprecedented level in the year 2039. To make matters worse, powerful enemies resembling old wartime vessels called the Fleet of Fog roam the waters, severing communication and transit to various regions.

Any attempt at retaliation ends in failure with humanity's current weaponry. Only Gunzou Chihaya stands a chance against the Fleet of Fog as captain of the friendly Fog I-401 submarine Iona. As a result, Gunzou and his crew, known as Blue Steel, are tasked with a critical delivery mission by the Japanese government: they must deliver humanity's last hope against the Fleet of Fog, the Vibration Torpedo Warhead, through hostile waters to the United States for mass production.

Though involved in the unsavory conflict, Blue Steel strives for nothing more than a peaceful resolution to it. As Iona undertakes the current mission and tasks beyond it, the crew upholds their values even in the face of harsh situations.