With no means for defeating Godzilla Earth, mankind watches as King Ghidorah, clad in a golden light, descends on the planet. The heavens and earth shake once again as the war moves to a higher dimension.

A vicious sniper has appeared in Tokyo, rendering the people too scared to go outside, once again it’s up to Conan to figure out the meaning behind the killings and capture the mysterious sniper before more lives are lost.

Humanity’s desperate battle to reclaim the Earth from Godzilla continues. The key to defeating the King of the Monsters may be Mechagodzilla, a robotic weapon thought to have been lost nearly 20,000 years ago.

In the year 2048, the human race is forced to leave Earth after decades of losing against Godzilla and other giant monsters. They take a twenty-year journey to another planet called Tau Ceti e, but upon arrival, they discover that the planet has become uninhabitable. As living conditions on their ship deteriorate, a young man named Haruo spearheads a movement to return to Earth and take it back from the monsters. The ship successfully makes the return voyage, but the crew realizes that twenty thousand years have passed, with Earth’s ecosystem having evolved to become centered around Godzilla.

Bombing case at Nichiuri TV in autumn. The Satsuki Cup, which crowns the winner of Japan’s Hyakunin Isshu, is currently being filmed inside the facility. The incident results in a big commotion and, while the building is burning to ashes, the only people left inside are Hattori and Toyama Kazuha. They get rescued just in time by Conan , who rushes to the scene. Both the identity and purposes of the bomber are unknown.

On a dark night, the Japanese police is raided by a spy. Different countries’ intelligence agencies—such as England’s MI6, Germany’s BDN, and America’s CIA—as well as the FBI’s secret files are going to be taken, but public safety officers lead by Tooru Amuro arrive just in time. The spy steals a car and escapes. The spy and Amuro are then locked in a dead heat on the highway, and just as it is about to cause an accident with multiple cars, the spy’s car is hit by FBI agent Shuichi Akai’s rifle bullet and falls of the roadway. The next day, Conan and his friends go to a newly-remodeled aquarium in Tokyo. Under the main attraction, a Ferris wheel, Conan finds an attractive woman alone and injured. Her left and right eyes are different colors.

Conan tries to track down Kaito Kid, who supposedly steals a replica of one of Van Gogh’s Sunflowers paintings during an auction.

The movie is set on a state-of-the art Aegis vessel with the full cooperation of Japan’s real-life Ministry of Defense and Maritime Self-Defense Force. The corpse of a Self-Defense Force member has been found — minus the left arm — and a spy has infiltrated the Aegis vessel. The heroine Ran is put in jeopardy, and Conan is forced to stand up against the dangerous Spy “X.”

Kogoro’s detective agency receives a mysterious phone call. Someone on the other end warns about a bomb and leaves behind a code, “The Boy in Blue and The Blue Zebra, the rain from above …” If Conan can decipher the riddle, he can stop the bomb. An adventure begins for Conan and the Detective Boys, taking place at a soccer match between Hideo Akagi of the Tokyo Spirits and Ryusuke Higo of Big Osaka

The Governor of Tokyo, Yuichiro Asakura, receives a threatening letter the day before the opening of Touto Line, a new train line for the Tokyo Metro. During the opening ceremony of the line, Conan Edogawa and the Detective Boys are driven by Professor Agasa and pass under the Touto Line. Conan, having heard about the threatening letter, notices explosives connected to the Touto railway; Using his original voice to inform the police as Shinichi Kudo, he is able to stop the train and divert traffic away from the explosives preventing any deaths.