Spirits are otherworldly entities with immense power, capable of creating spatial quakes whenever they appear. One way of dealing with them is through brute force and killing them... or making them fall in love and sealing their powers. Having sealed three Spirits, Shidou Itsuka continues his mission with Ratatoskr in locating more spirits and dating them, to ensure the world's safety from further destruction. However, this time around, their problems will not be limited to Spirits as a more imposing threat seems to have noticed their activities.

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.

When an extraterrestrial organism known as "Savage" attacks mankind, the only technology capable of combating the enemy is a weapon known as “Hundred.” A survivor of a Savage attack, Hayato Kisaragi is a teenager boasting the highest compatibility level with the aforementioned technology and as a result, is invited to master his skills at Little Garden, a prestigious military academy aboard a battleship. Over the course of his intense training for the battle ahead, he immediately attracts the interest of multiple female peers and gets drawn into a number of incidents as he tries to fight against the creatures that now inhabit Earth and threaten its safety.

The Sakurada siblings live a normal life in a typical Japanese household. Well, that's what their father, the king, wants for them at least. As members of the royal family, each sibling possesses a unique ability, and over two thousand security cameras have been placed around town to make sure the children are safe and sound. Moreover, all nine of them have been designated as a potential successor to the throne with the decision that the next ruler will be selected through an election. However, for the timid Akane Sakurada, the third eldest daughter who wields the power to manipulate gravity, all of this attention is a complete nightmare. With all the cameras constantly monitoring the candidates and even broadcasting their actions on the Sakurada-dedicated news channel, she decides that if she becomes king, the cameras have got to go. But just how will she convince the public that she is the most suited to rule if she can't even overcome her own shyness?! Election season is in full swing as the search for the next king begins in Joukamachi no Dandelion.