Im Verlauf des 21. Jahrhunderts hat die Menschheit durch den in Folge der globalen Erderwärmung ansteigenden Meeresspiegel einen großen Teil der Landmasse verloren. Wie vom einsetzenden Chaos gerufen, tauchte plötzlich die Nebelflotte auf und beanspruchte die Herrschaft über die Hochsee. Die Menschheit scheint zu einem langsamen, qualvollen Tod verdammt zu sein.
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", All 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 Gunzō 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 Gunzō comes in contact with it, awakening Iona. After Iona reveals that she had instructions to serve under him, Gunzō agrees to join forces with her, and they flee together. Back to the present, Gunzō is approached by Ryūjirō 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, Gunzō 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.
Au début du 21ème siècle, la montée des eaux repousse l'humanité à l'intérieur des terres. Alors que l'homme aurait pu se déployer sur les mers plus vastes que jamais, une mystérieuse flotte, la flotte de la Brume, fait son apparition et empêche quiconque de s'aventurer sur l'océan. Très vite, la Brume empêche les continents de communiquer entre eux en détruisant tous les moyens de communication. Les armes humaines sont inefficaces contre cette menace. La seule chance de l'humanité est un navire de la flotte de la Brume passé du côté des humains, l'I-401, et son commandant, le jeune Gunzô Chihaya.
21世紀中盤、温暖化に伴う海面上昇により、人類は地上での版図を大きく失った。その混乱に呼応するかのように世界各地に現れた「霧の艦隊」にすべての海域を封鎖され、人類は 疲弊の一途をたどっていた ――。
士官候補生・千早群像の前に現れた「霧の艦隊」の潜水艦「イ 401」。敵であるはずの「イ 401」、そのメンタルモデル「イオナ」との出会いは彼に、そして人類に何をもたらすのか・・・?
21世纪初人类受到温室效应的影响失去了大部分陆地版图，此时，神秘的海雾大舰队突然出现封锁了所有航路，人类被驱逐出所有海域。在这之后，出现了一组奇怪但强势的组合，这是一艘有人类指挥的“海雾”——伊401，虽然人类曾早就捕获了“海雾”，但并不知道如何启动，直到这艘“海雾”在两年前遇到千早群像而甦醒，并且伊401的心智模型伊欧娜找到千早后带他离开。而此次，他们接到了移送人类新型武器的委托。
En un futuro cercano, la humanidad ha sido impulsada lejos de los mares y masas de tierra están fuertemente aislados unos de otros, con la llegada de la "Flota de la niebla"; AI controlado barcos que poseen tecnología superior y potencia de fuego. A pesar de los esfuerzos combinados de la ONU, la Flota de Niebla logran destruir toda oposición y sumir al mundo en un estado de agitación.
