Losing Maya has made Kongou go berserk. Absorbing Maya and light cruisers has given Kongou unprecedented power, which she uses to obliterate the Fog's U.S Pacific Fleet and now turns on 401. To save Kongou, Iona decides to go in alone...
I-401 has been hit with two corrosive torpedoes in an ambush by Iona's sister ships, I-400 and I-402. 401's repair programs are impaired by a special program that had been brought in by the torpedoes. As 401 sinks and Gunzou weakens from his injuries, Iona is forced to make a choice...
As missiles rain down on Iwo Jima, the Mental Models work together to withstand the attack from the Fog's East Patrol Fleet One. With their help, I-401 manages to break through the blockade, but Kongou is hot on their heels...
The I-401 returns to Yokosuka to pick up the secret weapon developed by the Japanese Government.
The battle against the battleships Haruna and Kirishima begins with the I-401 drawing them to a trap set at the ruins of the old Yokosuka city.
The I-401 and her crew reach the Yokosuka Base for repairs and resupply. Gunzō takes Iona for a visit to the memorial for the Navy soldiers that died in the war against the Fleet of Fog.
By 2039, global warming had caused sea levels to rise and large amount of territory to be lost. As though in response, a mysterious group of warships clad in mist, “the Fleet of Mist,” appeared in every corner of the ocean, and began attacking human ships. In spite of humanity mustering all their strength, they were utterly defeated by the Mist's overwhelming force. All of humanity's trade routes were blockaded by the Fleet of Mist, their political economy was destroyed, and the human race was steadily beaten down. Seven years later, the Fleet of Mist's submarine I-401 appears before cadet Gunzo Chihaya. The humanoid life form that pilots the sub, who should be their enemy, is instead offering her services to mankind.