"Chiisai Sensuikan ni Koi o Shita Dekasugiru Kujira no Hanashi" centers on the unlikely relationship between a small submarine and a massive whale. The submarine, designed for underwater exploration, operates in a world where marine life and technology coexist in a delicate balance. The whale, significantly larger than the submarine, is portrayed as a gentle yet enigmatic creature with a deep connection to the ocean's mysteries. Their interactions form the emotional core of the story, exploring themes of communication, coexistence, and the boundaries between nature and technology.

The narrative unfolds as the submarine embarks on a mission to study the whale, initially driven by scientific curiosity. Over time, the submarine develops a profound emotional bond with the whale, transcending its programmed purpose. The whale, in turn, exhibits a sense of awareness and curiosity toward the submarine, creating a dynamic that blurs the line between machine and living being. The story delves into the challenges of their relationship, including the physical limitations imposed by their size difference and the broader implications of their connection within the marine ecosystem.

Supporting characters include researchers and engineers who monitor the submarine's mission, providing context for the technological and environmental themes. Their perspectives highlight the ethical and practical dilemmas of integrating advanced technology with natural ecosystems. The series balances moments of introspection with action-driven sequences, as the submarine and whale navigate underwater hazards and external threats that test their bond.

The plot progresses through a series of episodic encounters, each revealing new layers of the submarine's and whale's personalities and their evolving relationship. The story culminates in a climactic event that forces both characters to confront the consequences of their connection, ultimately raising questions about the future of their coexistence. The series maintains a neutral tone, allowing the narrative to explore its themes without overt moralizing, making it accessible to a wide audience.