Extraterrestrial beings known as Trench Walkers appear from Antarctica and begin to terraform the planet. They raise the sea level by seventy meters, submerging major cities like Tokyo, and transform the world's water into a substance called Nectar that is lethal to most humans. A small number of girls who are biologically compatible with Nectar are recruited to pilot submarines and wear special combat swimwear, forming the Masakado Girls Academy Submarine Fleet to fight back and reclaim the Earth.

The story follows Hiro Todoroki, a quiet but determined girl whose older sister, Shino Todoroki, served as a submarine fleet captain and died in battle against the Trench Walkers. Before her death, Shino left Hiro a message urging her to find the legendary marine Kiriri Tsunoba. Following that directive and wrestling with her own doubts, Hiro sets out to join the Masakado Girls Academy Submarine Unit.

Once enrolled, Hiro undergoes training and is assigned to a team alongside Kiriri, a fierce and experienced soldier who fought alongside Shino. In their first major engagement, the human allied fleet launches an encirclement operation against a Trench Walker horde. Hiro and her squad are deployed as decoys, and they find themselves at risk of being caught in their own side's bombardment. In a moment of desperation, Hiro devises a bold counter-plan that Kiriri approves, turning the tide and allowing the operation to succeed.

After this victory, a new superweapon is deployed: the submarine Naotora, armed with a massive Nectar cannon designed as a trump card against the invaders. Hiro, Kiriri, and other veteran members of the White Shark Unit are assigned to the Naotora and head to a fortified sea gate in Australia. From there, they launch a campaign to push directly into the Trench Walker stronghold in Antarctica, setting the stage for the final confrontation to determine the fate of the Earth.