On their way to a singing contest, Mai and Saki meet a mysterious man looking for the oldest clock in town. It turns out that this clock is a portal to the World of Clocks, and the mysterious man is a servant of Dark Fall who wants to stop time to destroy the world. With the help of the clock spirits, Pretty Cure must fight to escape his perfect maze and start time flowing again. Takes place during the second half of Futari wa Precure Splash☆Star.

Kudou Shinichi is living his life as Edogawa Conan, but those days seem like they might end pretty soon. The Black Syndicate is coming dangerously close to learning the truth about Shinichi having survived. Conan and everybody around him may end up dead if he doesn't manage to find Irish—a member of the Black Organization who has infiltrated the police forces, currently investigating a big serial murder case.

The warship Aegis Destroyer is conducting public exercises in Maizuru Bay where, coincidentally, a suspicious foreign ship was recently spotted. Conan Edogawa, Ran Mouri, Kogorou Mouri, Sonoko Suzuki, and the Detective Boys all receive a ticket to attend this event. However, while the ongoing military operations are underway, one of the crew members comes across a lieutenant's severed left arm. Conan later discovers that a foreign spy may have infiltrated the warship to obtain classified information by any means necessary. If the information were to leak, Japan's line of defense would be exposed, leaving the country unprotected from hostile attack.

With the help of the police at sea while other friends and allies investigate on the mainland, Conan must now prevent this national crisis and identify the spy for the sake of Japan.

[Written by MAL Rewrite]

The momentous day of the opening of the new Tokyo subway, the Touto Line, has come, but a bombing incident puts all celebrations to a halt. The governor of Tokyo is caught in the blast while onboard the train, but he and everyone else present is fortunately saved by the quick thinking and actions of Conan Edogawa.

Intrigued by the incident, Conan researches the governor's political history and discovers that the man was responsible for the destruction of a village in Niigata to build the Kitanosawa Dam. Believing the attack to be related to the construction of the dam, Conan, accompanied by Ran Mouri, Kogorou Mouri, Professor Agasa, Sonoko Suzuki, and the Detective Boys, decides to visit the village and investigate. 

There, they meet a group of locals who lived in the old village before it was torn down. However, just as one mystery leads to another, one of the locals is murdered. Suspecting that something much more sinister is afoot, Conan vows to uncover the truth behind these two incidents before it is too late.

[Written by MAL Rewrite]