"Blue Submarine No. 6" is a four-episode OVA series set in a post-apocalyptic world where Earth's surface has been largely submerged due to rising sea levels caused by global warming. The story revolves around the conflict between humanity and a race of genetically engineered marine creatures led by the enigmatic scientist Zorndyke. These creatures, known as the "Blue Water," have declared war on humanity, seeking to reclaim the planet for themselves.

The protagonist, Tetsu Hayami, is a former naval officer who is reluctantly called back into service to pilot the advanced submarine, Blue Submarine No. 6. Hayami is joined by a diverse crew, including the skilled and determined Mayumi Kino, the stoic and experienced Lt. Cmdr. Hijikata, and the young and enthusiastic Mutio, a hybrid human-marine creature who becomes a key figure in the narrative. The crew's mission is to locate and confront Zorndyke, who resides in a heavily fortified underwater base.

As the story progresses, the crew faces numerous challenges, including battles with the Blue Water forces and internal conflicts within their own ranks. The narrative explores themes of coexistence, environmental destruction, and the ethical implications of genetic engineering. Hayami's interactions with Mutio, in particular, highlight the potential for understanding and empathy between humans and the Blue Water, challenging the notion of an irreconcilable divide between the two species.

The climax of the series occurs when the crew finally reaches Zorndyke's base. Zorndyke reveals his ultimate plan: to create a new world where humans and marine life can coexist harmoniously, albeit under his control. The final confrontation forces the characters to confront their own beliefs and the consequences of their actions, leading to a resolution that leaves the future of both humanity and the Blue Water uncertain.

"Blue Submarine No. 6" combines elements of science fiction, action, and drama, presenting a thought-provoking narrative that delves into complex themes while maintaining a focus on character development and interpersonal dynamics. The series is notable for its blend of traditional animation and early CGI, which was groundbreaking at the time of its release.