The story begins when stage actress Juri Maki visits the detective Kogoro Mouri for help. She has received a cryptic note from the phantom thief Kaito Kid, who announces he will steal her prized star sapphire ring, known as the Jewel of Destiny, during the final performance of her play Josephine at the Sora Theater in Shiodome. Kogoro, along with Conan Edogawa, Ran Mouri, the Detective Boys, and others, attend the performance to guard the jewel. During the event, Kaito Kid appears disguised as Shinichi Kudo, taking advantage of his near-identical appearance to the missing high school detective. Conan pursues Kid onto the rooftop but is unable to capture him, and Kid escapes, leaving the jewel seemingly safe.

To thank them for protecting the ring, Juri invites the group to her villa in Hakodate, Hokkaido. They board a Sky Japan Boeing 747 flight. Among the passengers are the play's cast members, including Juri's current boyfriend Shinjo, the director Ban, actors Narusawa and Tajima, her manager Yaguchi, makeup artist Natsuki Sakai, and Ran's mother Eri Kisaki, who joins unexpectedly. During the flight, Conan realizes that Kid's original plan was never to steal the ring at the theater—the true target was the airplane itself, as the coded message in the note pointed to the flight number 865.

Shortly after takeoff, Juri eats a piece of chocolate and dies instantly from cyanide poisoning. Conan investigates and deduces that the poison was mixed into her makeup foundation. The culprit is Natsuki Sakai, Juri's makeup artist, who harbored deep resentment after Juri sabotaged her dream of working in Hollywood. However, before the case can be fully closed, the pilot and co-pilot collapse from cyanide poisoning as well—they had kissed Juri's hand earlier during a greeting, ingesting the poisoned makeup. With both pilots incapacitated, the actor Shinjo volunteers to take over the controls and asks Conan to assist him in the cockpit.

Conan quickly realizes that Shinjo is actually Kaito Kid in disguise. Kid confesses that he boarded the flight to steal the star sapphire but lost interest after discovering it was a fake. Now trapped together in a crisis, the rival detective and phantom thief must cooperate to save the 365 passengers on board. The plane struggles through a violent storm over Hakodate. A lightning strike damages the aircraft and causes a fire on the runway, making landing impossible. Fuel is rapidly leaking, leaving only minutes before the plane runs out.

With Kid's arm injured from the turbulence, he steps aside and Ran Mouri takes over the controls at his urging. Conan, speaking through a phone call in his true voice as Shinichi Kudo, guides Ran through the landing procedure. Ran reveals her feelings for Shinichi during the call, confessing that she loves him. Kid sacrifices his own escape to lure police cars toward a pier, using their headlights as makeshift runway lights. Ran and Sonoko Suzuki manage to land the damaged plane safely on a seaside berth in Muroran. After the landing, Ran is treated by a medic who, in a post-credits scene, reveals himself to be Kaito Kid in disguise. He praises her landing and vanishes before she can react.

The central characters include Conan Edogawa, the young detective in a child's body; Kaito Kid, the elusive phantom thief who serves as both rival and reluctant ally; Ran Mouri, whose emotional journey culminates in her confession to Shinichi; Kogoro Mouri, the bumbling detective; Eri Kisaki, Ran's mother who unintentionally becomes the voice of Conan's deductions; and the ensemble of theater cast members whose hidden grievances fuel the murder plot. The setting moves from a Tokyo theater to the confined space of an airliner and finally to a desperate nighttime landing in Hokkaido, creating a narrative that blends a locked-room murder mystery with a high-stakes disaster sequence. Key narrative arcs include the Conan-Kid rivalry turning into an uneasy partnership, the resolution of Juri's murder through forensic deduction, and Ran's emotional growth as she takes control of the plane and voices her long-held feelings for Shinichi.