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.

The continent of Atlatan once again finds itself devoured by the flames of war after a horrific event known as the Great Hall Tragedy. What was supposed to be a joyful occasion that would establish peace between the Fantasia Union and the Factory Alliance, the marriage of Sir Alexis Douse and Lady Marrine Kreische, was instead a tragedy. As the bride and groom walked down the aisle, the ceremony was suddenly interrupted by a powerful convergence of "Chaos," a dark energy from another dimension that corrupts the land and brings forth monsters and demons into the world. From within that energy appeared the Demon Lord of Diabolos, an evil being who instantly murdered the archdukes of both factions, shattering any hope for peace between them. Having failed to prevent this disaster, Siluca Meletes, an Alliance mage, is traveling through the Chaos-infested countryside to study under a master magician. When she is intercepted by a group of soldiers working with the Federation, Siluca is rescued by Theo Cornaro, a young warrior carrying a mysterious "Crest," a magical symbol that gives its wielder the ability to banish Chaos. Bearing no allegiance to a specific domain, Theo hopes to attain the rank of Lord so that he can liberate his home town of Sistina from its tyrannical ruler and the Chaos spreading within it. Impressed by his noble goal, Siluca enters into a magical contract with Theo, and the two embark on a journey to restore balance to their war-torn land.

The mutinous Musashi has been defeated, and the girls from Yokosuka Girls' Marine High School are safely back home. However, the Harekaze sustained critical damage during its final encounter with the Musashi and may not be able to sail again. Moreover, rumors spread that the Harekaze-class will be dissolved due to it lacking a ship. Other classes' attempts to scout members from the Harekaze's crew only make the situation even more uncertain. The answer to this dire problem may be found in the sealed orders that the secretary of the Harekaze, Kouko Nosa, is to deliver to its crewmembers. But time is running short...