Conan Edogawa is the pseudonym of Shin'ichi Kudo, but more than just a pseudonym, a pseudoform. Shin'ichi Kudo, an inquisitive seventeen year old student, was investigating a blackmail case when attacked by members of the Black Organization. He was forced to take an experimental APTX 4869 drug which caused, in a rare side-effect, his body to transform into that of a seven-year-old.

This does not stop Shin'ichi, adopting the name Conan Edogawa he moves in with Ran Mōri, his childhood friend and sweetheart. Enrolling in a elementary school to complete his disguise he vows to find out who is backing the Black Organization, and to have his revenge. With the help of his his oddball classmates, an ex-member of the Black Organization Ai Haibara, whose also been turned into a child, and his beloved he just might do it...

The games story follows the Conan through his school life which intertwines with his search for justice. He forms a Junior Detective League in his school to help him out. This cast of characters will help supply you information throughout the game.

The gameplay consists of using a map screen to travel to a number of areas collecting clues for the case you are on. Each area offers you the ability to examine the area, talk to bystanders, collect items, and sometimes attack if a threat is apparent.

After collecting information you will have the chance to open your notebook, which will cause the WonderSwan to switch to a vertical orientation, and review your information. Also in the note books is a logic grid. On the grid you will have to select where you've deduced something intersects,who was at the scene at what time, by marking it with a circle and voiding all impossibilities with crosses. Once you've completed an entire grid you'll be able to present your deductions or press a point further allowing you to progress. If you've gotten your reasoning wrong, however, it is back to the drawing board and time to recheck you evidence and maybe time to see if you missed some clues.

This game includes five scenarios, roughly translated to English as: