Kimika asks Jirokichi to help her open a trick box created by a mid-19th Century tinkerer. Inside the box is Luna Memoria, the world's largest moonstone left to her by her late husband. The instructions to open the box are written on a piece of paper stuck between the pages of one of ten thousand books given to Jirokichi. In order to lure Kaito Kid, Jirokichi puts the trick box containing Luna Memory on display. Conan and friends try to figure out how to open the box, while Kid lurks nearby in disguise...

Conan and his friends, along with assistant homeroom teacher Wakasa, discover a skeleton in the old storage shed at the school. The victim died approximately ten years earlier. Ten years ago, a group of four thieves broke into the home of a wealthy man and fled with 200 million yen worth of gold ingots. That same night, a group of suspicious figures were seen entering Teitan Elementary School. Conan and his friends attempt to crack the code written on the headband found in the skeleton's hand. Conan realizes the class schedule Ayumi found in the storage shed is the key to cracking the code.