15 years prior to the events of the film, during the World Sports Games (WSG) hosted in Boston, a series of alarming kidnappings took place. The victims were high-profile individuals, specifically the heads of companies who sponsored the event. The first person taken was the CEO of a confectionery company, followed by the CEO of a significant conglomerate. The final victim was Morgan Tracy, the CEO of an automotive firm, who managed to escape but was sadly shot dead while fleeing via the Detroit People Mover.
In the present day, beloved character Conan Edogawa (Minami Takayama), alongside his friends Anita, the Detective Boys, and Rachel, attends a revealing event for the Hyper Linear, an innovative vacuum superconducting train designed to reach astounding speeds of 1000 km/h. This remarkable train is set to make its inaugural journey coinciding with the Tokyo WSG Opening Ceremony, departing from Nagoya Airport to the stadium terminal. The event introduces Alan McKenzie (Charles Glover), the President of the WSG Committee and a former FBI Director. He anticipates taking the Hyper Linear on its maiden voyage accompanied by various sponsors and committee members, while a raffle allows select members of the public a chance to partake in this historic ride.
With the hopes of experiencing the Hyper Linear, the Detective Boys appeal to Serena, the daughter of a WSG sponsor, to secure them tickets. However, during the dinner buffet, a blackout occurs, and when the lights return, they discover that Samuel Sebastian, Serena's father, is missing. Detective Meguire and his team are swiftly called in to investigate. Conan uses his skills to deduce that Samuel was taken unconscious, hidden within a food cart in a kitchen cabinet.
In a police interview, Samuel shares that previously, a friend of his—a CEO—had been kidnapped while playing golf, making the investigators suspect a connection between the two incidents. During a visit to Agasa’s house, Serena expresses her gratitude to the Detective Boys by gifting them goodies. She managed to get six tickets for the Hyper Linear, but since there are seven in their group, an impromptu quiz is arranged to select who would join the trip, with Sonoko ultimately allowing the kids to go.
As concerns grow about the recurring kidnappings, Subaru Okiya (Ryotaro Okiayu) receives a call from the FBI, who are worried that the recent kidnappings bear similarities to the past Boston case. Together with Conan, they deduce that the next target is likely to be the CEO of an automobile company, which draws a connection to John Voit (Ryan Drees), a British automobile executive.
Tensions rise further as John Voit confides in Richard, indicating he knows he could be the next victim. Meanwhile, during a briefing for select guests headed for the Hyper Linear's inaugural trip, it becomes apparent that someone is planning to take advantage of this situation. When an explosion disrupts the event and gas fills the room, chaos ensues as guests collapse into unconsciousness.
In the wake of this incident, Conan cleverly places a GPS tracking device on John Voit, leading to a pursuit of the kidnappers. Subaru, recognizing the urgency of the situation, follows suit, while Masumi takes a keen interest in the unfolding events. As allied forces converge, revelations expose the deeper layers of betrayal—Maiko Shirahato (Aya Hirano), carrying a deep-seated grudge against Alan due to her father's wrongful conviction decades ago, prepares to exact her revenge.
As Conan and Masumi infiltrate the Hyper Linear, they discover Alan trapped and use this critical moment to alert others of the impending danger. A countdown intensifies the stakes as the train approaches its launch, and culminates in a dramatic last-ditch effort involving a giant flag designed to slow the train's momentum.
Amidst the chaos of the almost catastrophic event where the Hyper Linear derails, the film dovetails into heartfelt reunions and resolution of the deep personal conflicts driving the actions of its complex characters. Akai secures the climactic moment with a silver bullet intended to avoid severe collateral damage while ensuring Shirahato is incapacitated but not killed.
As the story reaches its conclusion, we witness Conan triumphantly saving the day, the bonds of friendship among all characters, and hints of lingering backstories waiting to be explored further in the beloved franchise. Ultimately, the tale highlights themes of justice, revenge, and the indomitable spirit of those—like Conan—who strive to keep the balance between right and wrong, while also delving into compelling character arcs that keep audiences captivated till the very end.