The story unfolds near Tokyo’s ISO facility, the Pacific Buoy, a state-of-the-art offshore Interpol hub designed to link global law enforcement camera feeds and test a revolutionary facial recognition technology. Conan Edogawa and the Detective Boys arrive on a VIP tour at the invitation of Sonoko Suzuki. Meanwhile, Haibara receives an ominous premonition after noticing Gin, a high-ranking Black Organization operative, lurking nearby.Tragedy strikes when an Interpol official stationed in Germany is assassinated by Vermouth, sparking immediate chaos. Driven by suspicion, Conan sneaks into the facility's central security room using his gadgets. He discovers that
the Organization, led by the enigmatic Gin, has infiltrated the facility and kidnapped a female European engineer. Their sinister objective is to steal the prototype facial recognition database, which possesses the terrifying capability to age-progress any human face across decades, effectively threatening Haibara’s
hidden identity as the shrunken Shiho Miyano.The Black Organization wastes no time leveraging the stolen data. Using the advanced software, they successfully age a childhood photograph of Shiho, matching her directly to Ai Haibara. Realizing the immense danger, the Organization abducts Haibara from a submarine docking bay, dragging her into the dark ocean depths aboard their stealth vessel. Conan resolves to rescue her, utilizing his turbo engine skateboard and scuba gear to launch a daring, high-risk pursuit into the freezing, pressurized depths of the sea.Inside the submarine, Haibara remains defiant, refusing to yield to her captors. Conan infiltrates the vessel alongside Shuichi Akai, who coordinates tactical sniper support from the surface, while Toru Amuro works from within the shadows to undermine the syndicate's communications. A tense, claustrophobic cat-and-mouse game ensues. Gin activates the facility's automated defense systems, turning the Pacific Buoy's powerful torpedoes against the rescue teams and threatening to obliterate the entire installation to cover their tracks.With the facility facing catastrophic destruction and time running desperately short, Conan orchestrates a brilliant counterattack. He uses his enhanced soccer ball and criminal-tracking glasses to manipulate the submarine's torpedo trajectory, forcing the vessel to misfire and crippling its propulsion systems. As the ocean threatens to swallow the collapsing Buoy, Akai delivers a decisive sniper shot that neutralizes the immediate Black Organization threat, allowing Conan to orchestrate a daring underwater extraction. He successfully rescues Haibara from the sinking wreckage, bringing her back to the surface just as dawn breaks. In a breathless climax, the heroes survive the devastating implosion, preserving the secret of Conan’s true identity while leaving the shadowy syndicate licking their wounds, utterly defeated yet dangerously plotting their next inevitable vengeance from the dark.