"Undersea Super Train: Marine Express" is a feature-length anime film set in a futuristic world where advanced technology and underwater exploration are central to the narrative. The story unfolds aboard the Marine Express, a luxurious submarine train traveling through an intricate network of underwater tunnels. The train is en route to the underwater city of Marinapolis, a thriving metropolis beneath the ocean. The journey becomes the backdrop for a series of interconnected events involving a diverse group of passengers, each with their own motivations and secrets.

The protagonist, a young boy named Hanaichi, boards the Marine Express with his pet dog, Pochi, and quickly becomes entangled in a mysterious plot. Hanaichi encounters a variety of characters, including a scientist, a journalist, a wealthy businessman, and a group of criminals. The criminals, led by the enigmatic Dr. Shizuma, plan to hijack the train and use its advanced technology for their own nefarious purposes. Their goal is to disrupt the underwater city's infrastructure and seize control of its resources.

As the journey progresses, tensions rise among the passengers, and alliances shift. Hanaichi, with his innate curiosity and resourcefulness, becomes a key figure in uncovering the criminals' plans. Alongside him, the journalist and the scientist work to piece together the truth, while the businessman's true intentions remain ambiguous. The narrative weaves together themes of trust, betrayal, and the ethical implications of technological advancement.

The climax occurs as the Marine Express approaches Marinapolis, with the criminals attempting to execute their plan. Hanaichi and his allies must confront Dr. Shizuma and his gang in a high-stakes showdown. The resolution hinges on the cooperation of the passengers and the ingenuity of the protagonists, ultimately leading to the preservation of the underwater city and the thwarting of the criminals' scheme.

The film explores the dynamics of its ensemble cast, with each character contributing to the unfolding drama. Hanaichi's innocence and determination serve as a counterpoint to the morally ambiguous actions of other passengers, creating a layered narrative that balances action, mystery, and interpersonal conflict. The underwater setting and the advanced technology of the Marine Express provide a visually rich and imaginative backdrop for the story, emphasizing the intersection of human ambition and the natural world.