"High School Fleet" is set in a world where Japan has become a maritime nation due to rising sea levels, and young women are trained to become skilled sailors known as "Blue Mermaids." The story centers on Akeno Misaki, a cheerful and determined girl who enrolls at Yokosuka Girls' Marine High School to fulfill her dream of becoming a Blue Mermaid. She is appointed captain of the training ship Harekaze, a position she initially feels unqualified for but grows into as the series progresses.

The narrative begins with Akeno and her classmates embarking on their first training voyage. However, their routine mission takes a dramatic turn when they receive a distress signal from another ship. Upon investigating, the Harekaze crew is falsely accused of mutiny and attacking their own fleet. This misunderstanding forces them to go on the run, navigating treacherous waters while evading pursuit from both the Blue Mermaids and hostile forces. The crew must work together to clear their names, uncover the truth behind the conspiracy, and protect their ship.

Key characters include Akeno Misaki, whose leadership skills and optimism inspire her crew; Moeka China, the dependable vice-captain and Akeno's childhood friend; and Mashiro Munetani, the ship's navigator, who provides calm and strategic thinking. Other notable crew members include the skilled engineer Shima Tateishi, the resourceful communications officer Runa Suruga, and the talented gunnery officer Mei Irizaki. Each character contributes unique skills and personalities, fostering a sense of camaraderie and teamwork essential to their survival.

The series blends elements of naval warfare, mystery, and slice-of-life, with a focus on the challenges of leadership, trust, and perseverance. The crew faces numerous obstacles, including battles with enemy ships, internal conflicts, and the emotional toll of being labeled traitors. As the story unfolds, the Harekaze crew uncovers a larger conspiracy involving the manipulation of the Blue Mermaids' command structure, forcing them to confront powerful adversaries while staying true to their ideals.

"High School Fleet" combines action-packed naval battles with heartfelt moments of friendship and growth, creating a compelling narrative that explores themes of responsibility, loyalty, and the pursuit of justice. The series balances its high-stakes plot with lighthearted interactions among the crew, making it an engaging and dynamic story.