Born from a cocoon in the village of Old Home, a young Haibane—a being with a halo and small gray wings—awakens to a world she does not understand without memories of her past. Named Rakka for the dream of falling she had while inside the cocoon, she soon becomes accustomed to life in the strange town. However, there are strict rules for the Haibane, such as being forbidden to leave the village or go near the walls surrounding it. These, along with mysterious disappearances of their kind on their Day of Flight, begin to unsettle Rakka and the others since they know almost nothing about their own kind. As Rakka and the other Haibane live their lives with no memories of the past, they try to break free from their former pain and ultimately find salvation.

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...

The story follows Benio Haikara-san Hanamura, who lost her mother when she was very young and has been raised by her father, a high-ranking official in the Japanese army. As a result, she has grown into a tomboy—contrary to traditional Japanese notions of femininity, she studies kendo, drinks sake, dresses in often outlandish-looking Western fashions instead of the traditional kimono, and is not as interested in housework as she is in literature. She also rejects the idea of arranged marriages and believes in a woman's right to a career and to marry for love. (Source: ANN)

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.