"Detective Conan: Kurogane no Submarine" is a feature-length anime special that centers on a high-stakes mystery involving advanced technology and international intrigue. The story begins with Conan Edogawa, Shinichi Kudo in his child form, and his allies investigating a series of suspicious incidents tied to a cutting-edge submarine developed by a Japanese defense contractor. The submarine, named Kurogane, is equipped with revolutionary stealth capabilities, making it a target for espionage and sabotage.

The narrative unfolds as Conan, along with his friends from the Detective Boys, Ran Mouri, and Kogoro Mouri, are invited to a demonstration of the Kurogane submarine. During the event, a key scientist involved in the project is found dead under mysterious circumstances. Conan deduces that the death is linked to a larger conspiracy involving foreign agents attempting to steal the submarine's technology. As the investigation deepens, Conan uncovers a web of betrayal, hidden agendas, and a race against time to prevent the submarine from falling into the wrong hands.

The plot intensifies when the submarine is hijacked by a group of infiltrators, forcing Conan and his allies to board the vessel to stop the perpetrators. Inside the submarine, Conan faces numerous challenges, including deciphering cryptic clues, outsmarting the hijackers, and ensuring the safety of the crew and his friends. The story highlights Conan's deductive prowess and resourcefulness as he navigates the confined and dangerous environment of the submarine.

Key characters include Conan Edogawa, whose sharp intellect drives the investigation; Ran Mouri, who provides emotional support and occasional assistance; and Kogoro Mouri, whose comedic ineptitude contrasts with Conan's brilliance. The antagonist, a shadowy figure orchestrating the hijacking, is revealed to have personal motives tied to the submarine's development, adding layers to the conflict.

The narrative builds to a climactic confrontation where Conan must use his wits and the submarine's advanced systems to outmaneuver the hijackers and prevent a catastrophic outcome. The resolution ties together the various threads of the mystery, revealing the true mastermind behind the conspiracy and restoring order. The story concludes with the submarine's technology safeguarded and the characters reflecting on the events, setting the stage for future adventures.