The alien Abyssal Fleet continues to threaten humanity, and the Kanmusu—girls endowed with the spirits of Japanese warships—are mankind's last hope. With their ongoing struggles, the Kanmusu are almost certain to sink below the waves into their demise. The Mutsuki-class destroyer Kisaragi is one of the unfortunate ships to meet such a fate.

However, following a successful night raid, the Eighth Fleet's Kanmusu spot Kisaragi alive but unconscious, floating to the sea surface. But the anomalous situation and Kisaragi's strange behavior leave Kanmusu cautious of her. Furthermore, the other ships start to hear mysterious voices and come across crimson waters that damage their equipment. Strangely, Fubuki, the lead ship of the Fubuki-class destroyers, appears unaffected.

As Fubuki and the other Kanmusu tackle the unusual occurrences around them, the harsh reality of their existence and the Abyssal Fleet begins to unravel. Even so, the girls must keep facing forward to liberate the sea and protect those they cherish the most.