In the near future, mankind was driven away from the seas and landmasses were isolated from each other with the advent of the "Fleet of Fog", AI controlled ships which destroyed all opposition turning the world into turmoil. Years later, the Japanese Government is about to launch an unmanned cargo shuttle into orbit when the Fleet of Fog ship Nagara appears to prevent it. The launch is a success when the human-crewed Fog submarine I-401 defeats the enemy by request of the government. After the battle, the I-401's captain Gunz? Chihaya reminisce with its mental model, a human-shaped avatar called Iona about their first meeting two years ago. It was during this time that I-401 was under human custody for years, but unresponsive until Gunz? comes in contact with it, awakening Iona. After Iona reveals that she had instructions to serve under him, Gunz? agrees to join forces with her, and they flee together. Back to the present, Gunz? is approached by Ry?jir? Kamikage, the Assistant Secretary of Military Affairs, who reveal that the shuttle was destroyed before accomplishing its task, which is to deliver the plans of a new weapon developed to fight the ships of the Fog to the United States, as Japan now lacks the resources needed to mass produce it. Accepting the task of crossing the Pacific Ocean to take the plans to the US by themselves, Gunz? and his crew depart to resupply at the Yokosuka Base, but the Fog's Heavy Cruiser Takao takes heed of the I-401's approach and prepares itself to engage it.