"Tristia of the Deep Blue Sea" is set in a fantastical world where advanced technology and magic coexist, centered around the floating city of Tristia. The city, once a thriving hub of innovation and prosperity, faces decline after a catastrophic event known as the "Great Collapse." The story revolves around Nanoca Flanka, a young and talented engineer who dreams of restoring Tristia to its former glory. Nanoca inherits her late grandfather's workshop and dedicates herself to reviving the city's lost technologies, particularly the ancient automata, mechanical beings that once served as the backbone of Tristia's infrastructure.

Nanoca's journey begins when she encounters Panavia, a mysterious automata who awakens after years of dormancy. Panavia becomes Nanoca's companion and protector, aiding her in her quest to rebuild Tristia. Together, they face numerous challenges, including rival engineers, political intrigue, and the remnants of the Great Collapse that continue to threaten the city. As Nanoca delves deeper into her grandfather's research, she uncovers secrets about Tristia's past and the true nature of the automata, which hold the key to the city's survival.

The narrative explores themes of perseverance, innovation, and the balance between progress and tradition. Supporting characters include Forte Stollen, a skilled engineer and Nanoca's rival, and Viola, a resourceful merchant who provides assistance and resources. The story progresses through a series of engineering challenges, battles against mechanical threats, and the gradual unraveling of Tristia's history. Nanoca's determination and ingenuity drive the plot forward as she works to overcome obstacles and inspire hope among the city's inhabitants.

The series blends elements of steampunk and fantasy, with a focus on mechanical engineering and the ethical implications of creating sentient machines. The interplay between human ambition and the consequences of technological advancement forms a central conflict, as Nanoca strives to honor her grandfather's legacy while forging her own path. The story concludes with a resolution that ties together the threads of Tristia's past and future, leaving the city on the brink of a new era.