Due to Rising Seas, most of the land is lost, fleets of sentient warships mysteriously appear and devastate the world's navies. The Blue Steel submarine defects to the human side to help fight back.
Kongou obliterates the ships of the American Fleet of Fog and Iona, along the other mental models, make contact with Kongou in an attempt to bring her to her senses. However, Kongou claims that it's her duty to prevent further anomalies to the Fog by destroying Iona and all ships who come in contact with her, including herself, before locking down all communications. After barely deflecting an attack of Kongou's enhanced Super Gravity Cannon, the I-401 conceals itself, knowing that confronting her directly is useless, when Iona decides to reach Kongou and confront her face to face. Gunz? agrees with her plan and after evading a massive barrage of attacks, Iona boards a torpedo to reach Kongou's deck. Iona attempts to reason with Kongou who keeps attacking her until she finally traps Iona and prepares to self destruct herself to kill both, when the sequence is disrupted by I-401's Super Gravity Cannon. In the end, Iona suceeds to dissuade Kongou and prevents the destruction of both. The reformed Kongou befriends Iona while the superstructure created by her collapses. Days later, as the I-401's crew delivers the vibration warhead to the U.S. Navy as intended, Takao's body is restored and they return to the sea, hoping that their actions have helped change the world for the better.
On their way to Hawaii, their next stop of their journey to deliver the vibration warhead in San Diego, the restored and upgraded I-401 is chased by several Nagara class ships that are surprised and sunk when Gunz? orders an unexpected maneuver to sweep them all at once. After the battle, it is revealed that despite losing her physical body, Takao's core is still intact and she is now part of the I-401's systems. However, knowing that they are still being followed by I-400 and I-402, Gunz? decides to confront them. Before the battle, Iona's sisters make contact with her asking for her true intentions but she claims it is too difficult to explain with words. Meanwhile, an imprisioned Kongou breaks free and absorbs Maya along all the other ships around her. To confound their enemies, the I-401 moves forward along two decoys with increased capabilities, thanks to Hyuga, Haruna and Kirishima's direct control over them. After exchanging some fire, Iona contacts her sisters asking them to stop pursuing them before it is too late but they refuse to comply. When I-400 is about to be stricken by surprise, I-402 sacrifices herself to protect her sister, who despite finding this decision illogical, becomes driven into anger, leading her to fall into a trap set by the decoys and her defeat as well. Despite grieving for her lost sisters, Iona maintains her resolve to follow Gunz? to the end. However, the I-401 is soon after approached by a dozen ships from the American Fleet of Fog at the front, and a massive flying object at the back, composed of several fused ships led by Kongou, who claims that she wlll be the one who will sink I-401.