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... 
 
(Source: MAL Rewrite)

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. 
 
(Source: MAL Rewrite)

The students of four marine high schools, including Yokosuka Girls, participate in an operation to prevent pirates manning a heavily-armed seafort from making its way to Japan. During this time, Mashiro struggles with an important decision: to become the captain of a ship or stay with the Harekaze and her friends.

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