On the planet Zora exist two societies: the Innocent, an advanced culture that lives in domed cities, and the Civilians, who are forced to live in the harsh desert wilderness. As dictated by the Innocent, any Civilian that commits a crime is forgiven if they are not brought to justice within three days. Civilian Jiron Amos seeks revenge on the villainous outlaw Timp Sharon who murdered his parents, despite the fact the three-day period has long since passed. Hoping to get his revenge by stealing the mecha Xabungle from the merchant Carrying Cargo, Jiron teams up with a group of bandits known as the Sandrats and kidnaps Cargo's daughter Elchi, who ends up being sympathetic to his cause. Jiron's quest for revenge soon grows into a conflict much bigger—one that will eventually see the Civilians rise up against the Innocents' rule. [Written by MAL Rewrite]

In ancient times, the continents of Atlantis and Mu fought a war, and Atlantis lost. After losing the war, Atlantis transformed itself into a small planet and timeslipped to the present-day to try to take over the world again. But five warriors from Mu assemble on Easter Island, and together with giant cyborg white whale that houses the brain of the ancient queen of Mu, fight Atlantis off at various famous ruins around the world.

This time's location is set in the sea near the Hachijo-jima island, Tokyo. Engineers from around the world have gathered for the full-scale operation of "Pacific Buoy," an offshore facility to connect security cameras owned by the worldwide police forces. A test of a certain "new technology" based on a face recognition system is underway there. Meanwhile, Conan and the Detective Boys visit Hachijo-jima at Sonoko's invitation and receive a phone call from Subaru Okiya informing them that a Europol employee was murdered in Germany by the Black Organization's Jin. Conan, who is disquieted, sneaks into the facility and finds that a female engineer has been kidnapped by the Black Organization...! Furthermore, a USB drive containing certain information in her possession ends up in the hands of the organization... A black shadow also creeps up on Ai Haibara ...

Continuation of the Bikkuriman Series. Genki Seihikari and his friends join the adventure in order to save seven gods of the White Galaxy.