At Maizuru Bay, coast guard Masaaki Kurata spots a suspicious boat during a routine patrol. A careful inspection uncovers explosives hidden aboard, triggering an urgent report to the Wakasa Coast Guard. The incident quickly becomes news, with authorities noting that the vessel likely crossed into Japanese waters and carried components not manufactured in Japan, hinting at a broader threat.
Later that morning, Conan Edogawa, Ran Mouri and Kogoro Mori, along with Sonoko Suzuki and the Detective Boys, board the Atago-class destroyer to witness public military exercises after winning tickets. They are invited into the ship’s Combat Information Center (CIC), where a simulated air-to-air engagement is run. After the two prepared targets are “shot down,” alarms sound as a real sonar contact closes in on the vessel, prompting the captain to order a full search of the area.
Conan, joined by Ai Haibara who is in Osaka, suspects that a spy, codenamed X, may be among the passengers aboard. While the crew scans the waters, Conan also notices a sick boy known to a nearby man as “Yuki-kun,” hinting at a missing guardian and adding a personal thread to the mystery. Nanami Fuji, a crew member wearing the captain’s insignia, catches Conan’s attention as well.
In Osaka, Heiji Hattori receives a call from Conan and heads to Maizuru with Kazuha Toyama to dig deeper. They locate the body of a lieutenant whose hand had been severed; Heiji notices a red stain on the neck and deduces the body drifted to Osaka after the arm was separated at Maizuru.
On the ship, investigators from the Tokyo Metropolitan Police and Wakasa arrive with an autopsy report stating the victim died by drowning between 4 AM and 6 AM. A phone recovered from the body reveals a last email after 9 PM and a final call at 5:30 AM, while an empty microSD slot hints at a missing data card that could be the target of the leak. Conan deduces that the man seen with Yuki Harbor was the killer’s target, and that Nanami Fuji is connected to the ship’s security apparatus and the intelligence unit.
Conan spots Nanami Fuji attempting to monitor the investigation and quietly engineers a ruse to coax her into revealing herself, then compels her to disclose what she knows about the microSD card. The Intelligence Security Command is soon drawn into the case, confirming that X is suspected of targeting restricted information about the Aegis-class Destroyers.
Further investigations reveal that in the morning the victim waved a Japanese flag at Maizuru Harbour, and confidential destroyer data had been leaked to a shell company connected to a spy named Takekawa, who was spotted in Kyoto. Heiji and Kazuha track Takekawa to a warehouse in Osaka; Takekawa shoots Kazuha, but Heiji dives in and takes the bullet for her. Osaka Police quickly arrest Takekawa on the spot.
Back on the ship, Conan deduces that the man who claimed to be Yuki’s father is actually X, and urges Yuki to hide. X attempts to silence Conan but flees as there are too many civilians nearby. Yuki stops Conan from pursuing, fearing for his real father’s safety. X destroys the footage and takes Yuki hostage, but Ran spots him and leads the police to a crew member who is being held. Yuki identifies X’s real identity as a spy, and Ran fights X but is knocked overboard. Yuki then guides the police to X, who takes another crew member hostage. Conan kicks a soccer ball from his belt and knocks out X.
Conan stuns Kogoro with a device on his wrist and explains the truth about the body. He reveals that [Masaaki Kurata] had killed Sasaura, with an audio file of metallic clinking sounds matching the moment when Kurata’s baton struck his gun used as evidence. Kurata is arrested for obstructing the investigation.
Shortly after, the Detective Boys, Yuki, and Sonoko inform the larger group that Ran has disappeared. The police disclose that X admitted throwing a high-school aged girl with karate skills overboard during the fight. Realizing that Ran was the one thrown overboard, the destroyer turns around to search the last known location. A helicopter is dispatched to locate her, but initially cannot find her. Remembering Mori’s golden business cards she had kept, Conan directs the helicopter to follow the glittering trail—scattered cards floating on the sea—and Ran is eventually rescued alive.
As Conan prepares to leave, Nanami Fuji asks who he really is. Conan replies, in his characteristic, understated manner, that he’s just a typical elementary school student, and dashes off, leaving Nanami to wonder about the enigmatic boy she just met.
