A hundred years after catastrophic shifts in tectonic plates caused most of its area to submerge, Japan now thrives as a maritime nation. High functioning cities line the coasts of Japan, and well developed sea routes are defended by specialized naval ships. The marine industry is flourishing, and young girls are eager to join the Blue Mermaids—highly skilled women who devote their lives to protecting the seas. After some time apart, childhood friends Akeno Misaki and Moeka China are reunited at Yokosuka Girls' Marine High School. Here they are joined by others who share their dream of becoming Blue Mermaids. Soon, training exercises commence, with Akeno and Moeka being put in charge of their own ships and crew. Everything is progressing smoothly for Akeno as she settles into her role as captain and builds camaraderie between her fellow crew members aboard the Harekaze, a destroyer ship. However, unexpected engine and navigation failures soon leave their ship stranded and the crew in danger. High School Fleet follows the Harekaze's valiant crew as they navigate treacherous waters and other obstacles on their quest to become fully fledged Blue Mermaids.

While reveling in the successful clinching of a prized vase for his collection, Yoshifumi Nitta, a yakuza member, is rudely interrupted when a large, peculiar capsule suddenly materializes and falls on his head. He opens the capsule to reveal a young, blue-haired girl, who doesn't divulge anything about herself but her name—Hina—and the fact that she possesses immense powers. As if things couldn't get any worse, she loses control and unleashes an explosion if her powers remain unused. Faced with no other choice, Nitta finds himself becoming her caregiver. To let her use her powers freely, Nitta asks Hina to help out with a construction deal, which goes smoothly. But while this is happening, a rival yakuza group covertly attacks his boss. To Nitta's shock, his colleagues later pin the blame on him! Tasked with attacking the rival group in retaliation, Nitta steels himself and arrives at their hideout. But suddenly, Hina unexpectedly steps in and helps him wipe out the entire group. As it turns out, Hina might just become a valuable asset to Nitta and his yakuza business, provided she does not use her powers on him first! And so the strange life of this unusual duo begins.

One day, a city suddenly disappears. Takuya, a professional by-the-contract courier and lone wolf, meets Yuki, the only survivor from the city's extinction. The two rely on a message from Yuki's father, who was heard to be missing, and head toward the disappeared city, Lost. However, unexpected obstacles strike before the pair, with the reality especially shocking for Yuki. Before them are the feelings of those left behind, a mysterious group manipulating in the shadows, and unveiling the hidden conspiracy. Takuya and Yuki, who both were initially strangers, would deepen their bond during the journey and unravel the mystery of the Lost city. (Source: MAL News)