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.

One day after school, first-year high school student Yomogi Asanaka comes across a starving man under a bridge. Introducing himself as Gauma, the strange drifter informs Yomogi that he is a kaiju user, a person who deals with the kaiju—monsters who bring harm to the city and its citizens. The following evening, Yomogi runs into Gauma and his classmate Yume Minami. Simultaneously, a kaiju appears in a populated area of the city. Due to Gauma's lack of experience controlling the kaiju, he brings out a mysterious object from a glowing pouch, summoning a giant robot known as Dynazenon. Requiring the cooperation of four people, the mecha drags Gauma, Yomogi, Minami, and Koyomi Yamanaka—an unemployed man who was wandering on the street—into its cockpit. Their encounter with the kaiju marks the beginning of their entanglement with kaiju eugenicists—kaiju users who manipulate kaiju with ill intent—and their efforts toward bringing out the full potential of Dynazenon.

In Vandread, men are from Mars and women are from Venus! Well, not quite. Technology has allowed mankind to colonize the entire Milky Way galaxy, and in one star system, the men and women live on two different planets, Taraak and Mejere. A bitter and very literal gender war rages, to the point where they don't even see each other as the sames species anymore! Hibiki Tokai, a male third-class laborer from Taraak, ends up stuck on a battleship after a botched attempt at stealing a robot. When female pirates capture the Taraakian Vanguard, things don't look like they could get any worse for Hibiki. Unfortunately, they do; when the male crew of the Vanguard fire on their captured vessel out of desperation, they created a giant wormhole, which sucks the Vanguard and the Mejeran pirate's ships into itself! Now, stuck far away from their home planets, these men and women must learn to work together if they ever wish to make it back home.

This musical film is the visual realization of Discovery, an album by Daft Punk. It tells the story of a band of four extraterrestrial musicians who are kidnapped and brought back to Earth by an evil manager. Their only hopes lie with a space pilot from their home planet who, after receiving a distress call broadcasted during the abduction, seeks out to rescue them.