The Japanese government is about to launch an unmanned cargo shuttle into orbit when a ship from the Fleet of Fog appears to prevent the launch. The human-crewed submarine I-401 defeats the enemy by request of the government.

Takao blocks the I-401's path to Yokosuka by positioning itself inside the eye of a typhoon. After asserting that any attempts to avoid confrontation are too risky, Gunzō decides to take Takao head on.

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.

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 returns to Yokosuka to pick up the secret weapon developed by the Japanese Government.

As Tōjūrō passes away, Haruna decides to protect Makie and asks Kirishima's for help. Despite facing some heavy opposition, Haruna refrains from killing the attackers and orders Kirishima to flee with Makie, while she creates a decoy with her nano-machines.

I-401 heads to her secret home port with Makie, Haruna, and Kirishima on board. There, they find the heavy cruiser, Takao, waiting for them. As the crew prepare for their upcoming journey to the United States with repairs and supplies, they and the mental models learn a lot about each other...

Iwo Jima has been surrounded by the Fleet of Fog's Eastern Patrol Fleet 1. Gunzou invites the Mental Model of its flag ship, Kongou, ashore to the island to speak with her. Unable to accept the changes occurring to members of the Fog, Kongou blames Chihaya Gunzou and makes a critical decision...

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...

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...

Restored and strengthened by Takao's sacrifice, 401 forges on to America with 400 and 402 in pursuit. The sister ships face off in the waters of Hawaii. With enhanced specs, five Mental Models, and Gunzou's tactical prowess, the twin submarines are no match for the new 401... but Iona wishes them no harm.