"High School Fleet" is set in a world where Japan has become a maritime nation due to rising sea levels. 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," a prestigious role responsible for safeguarding the seas. The school trains students to operate ships, and Akeno is assigned as the captain of the training ship Harekaze, a destroyer crewed entirely by her classmates.

The narrative begins with Akeno and her crew embarking on their maiden voyage. However, their routine training mission takes a dramatic turn when they receive a distress signal from another ship. Upon investigating, they discover that the ship has been overtaken by a mysterious force, and its crew has turned hostile. The Harekaze is falsely accused of being involved in the incident, leading to a nationwide manhunt. Akeno and her crew must navigate treacherous waters, evade capture, and uncover the truth behind the conspiracy while proving their innocence.

Key characters include Akeno Misaki, whose leadership and optimism inspire her crew; Moeka China, the skilled and level-headed vice-captain; Mashiro Munetani, the diligent and resourceful navigator; and Shima Tateishi, the cheerful and reliable chief engineer. Each crew member contributes unique skills to the team, fostering camaraderie and teamwork as they face various challenges.

As the story progresses, the crew encounters other ships, allies, and adversaries, each with their own motivations and secrets. The series blends elements of naval warfare, mystery, and slice-of-life, exploring themes of friendship, responsibility, and perseverance. The Harekaze's journey is marked by intense battles, strategic maneuvers, and emotional moments as the crew works together to overcome obstacles and protect their ship.

The plot delves into the broader implications of the maritime world, including political intrigue and the ethical dilemmas of warfare. The series maintains a balance between action-packed sequences and character-driven storytelling, highlighting the growth and development of the crew as they navigate both literal and metaphorical storms. "High School Fleet" offers a compelling narrative that combines adventure, drama, and the unique setting of a maritime academy.