In the near future, a catastrophic shift in the world's climate has created a perpetual super cyclone in the Western Pacific known as the Grand Roar, which has ravaged the earth and flooded most countries. The sudden importance of shipping and navigation has led nations to hire escort cruisers to safeguard their investments from threats posed by ocean pirates. Hyousuke Nagimiya, a skilled system engineer, is tasked with upgrading the Pascal Magi, a ship crewed by an all-female crew led by Captain Misaki Nanaha. As they strive to prove themselves to their detractors, who view them as mere "Alice Brands" (a derogatory term for women in the industry), the crew becomes entangled in a larger global conspiracy that seeks to exploit the new world order.