On the shores of Tokyo Bay, a brand-new integrated resort and convention center named Edge of Ocean prepares to host an important Summit Meeting. Just before the event, tragedy strikes: an explosion erupts in one of the buildings, causing significant damage and resulting in the deaths and injuries of many Public Security Bureau personnel, including Toru Amuro and Yūya Kazami. Initial investigations reveal a shocking connection — a fingerprint found at the crime scene matches that of Kogoro Mouri, and evidence linked to his computer further implicates him. This leads to Kogoro's arrest, leaving his family and allies in distress.
As Ran Mouri and the others desperately seek legal help, they stumble upon Kyōko Tachibana, a freelance lawyer willing to defend Kogoro in court. Meanwhile, the Office of the Attorney-General perceives the evidence against Kogoro as compelling enough to proceed with prosecution, with Sayoko Iwai instructing Makoto Kusakabe to take on the case. During ongoing police investigations, it’s uncovered that key components — a gas valve and a pressurized cooker — can be connected through Internet of Things (IoT) technology and remotely manipulated via special networks such as Nor (similar to Tor). These devices were accessed from Kogoro's system, facilitating the explosion.
On the day of the conference, an unsettling pattern emerges: various IoT devices throughout Tokyo malfunction randomly, causing electrical shorts and fires across the city. Strangely, Kogoro remains in Tokyo Penitentiary, which makes his involvement in the bombing and IoT sabotage impossible, leading to the case against him being dropped.
Simultaneously, as preparations for a Mars-bound unmanned craft called "Hakuchō" are underway, Conan Edogawa deduces the identity of the real culprit behind both the explosion and the IoT chaos. The culprit is revealed to be Makoto Kusakabe, the prosecutor overseeing the case. Kusakabe had a close associate named Haba Fumikazu, who previously collaborated with Tachibana and was deeply in love with her. During the investigation, Haba was caught hacking into NAZU, a space agency similar to NASA, and was presumed dead after a tense interrogation by Toru Amuro, which led Kusakabe to seek revenge against the Public Security Bureau.
Amuro later reveals that Haba's death was staged to keep the public prosecutor from leveraging such allies again. Kusakabe’s plan escalates when he manages to hijack the missile capsule "Hakuchō," aiming to crash it into the Tokyo Metropolitan Police building. His reckless hacking causes a blackout and triggers a citywide IoT attack, forcing evacuation of personnel and residents to the Edge of Ocean. As time runs out, Kusakabe agrees to relinquish control but almost causes disaster. Conan, with assistance from Ai Haibara, Dr. Agasa, and the Detective Boys, orchestrates a daring plan: they use a drone built by Dr. Agasa to detonate the capsule near its launch point.
In a race against the clock and heavy traffic, Toru Amuro and Conan work together to shoot a projectile that deflects the missile, causing it to fall harmlessly into the water near the Edge of Ocean. With the capsule safely neutralized, the city is saved from catastrophe, demonstrating incredible teamwork and ingenuity amid a tense and complex investigation.
This story blends mystery, technological threats, and thrilling rescues, showcasing the resilience of friends and allies in the face of danger and deception.