"Aqua Planet Chronicle" is a science fiction manga set in a distant future where humanity has colonized a water-covered planet known as Aqua. The planet is almost entirely oceanic, with scattered floating cities and underwater habitats serving as the primary settlements. The story centers on the conflict between the surface-dwelling humans and the genetically engineered Aquans, a race of amphibious beings created to thrive in the planet's aquatic environment. Tensions arise as the Aquans demand independence and equal rights, while the human colonists seek to maintain control over the planet's resources.

The protagonist, Kaito Arisawa, is a young engineer working on the maintenance of the floating cities. His life takes a dramatic turn when he encounters an Aquan named Lune, a rebel leader fighting for her people's freedom. Kaito becomes entangled in the conflict after discovering a hidden truth about the Aquans' origins and the unethical experiments conducted by the human government. As the story progresses, Kaito and Lune form an uneasy alliance, navigating the moral complexities of war, identity, and coexistence.

The narrative explores themes of environmental exploitation, genetic engineering, and the ethical implications of creating sentient life. The human government's attempts to suppress the Aquans' uprising are met with escalating resistance, leading to large-scale battles both on the surface and beneath the ocean. Key characters include General Ryoma Takeda, a ruthless military leader determined to crush the rebellion, and Dr. Elena Voss, a scientist who harbors guilt over her role in the Aquans' creation. The story also delves into the Aquans' culture, their connection to the planet's ecosystem, and their struggle to define their identity separate from their human creators.

As the conflict intensifies, Kaito and Lune uncover a deeper conspiracy involving a secret human faction seeking to weaponize the Aquans for interstellar domination. The climax revolves around a race to prevent the activation of a doomsday device capable of devastating the planet's fragile ecosystem. The resolution sees both humans and Aquans grappling with the consequences of their actions, setting the stage for a fragile but hopeful coexistence. The manga balances action, political intrigue, and philosophical questions, creating a layered narrative that examines the cost of progress and the possibility of redemption.