Season 1

It has been reported that there were seven mysteries that exist in the Fudo High School, though only six of them had been solved. The high school student Hajime Kindaichi is invited by the Mystery Research Team leader, Ruiko Sakuragi to help her solve the seventh riddle. There is even a possibility that if the old school building is demolished, a man called "After-School Magician" will begin to murder.

Ruiko has been killed in the locked biology classroom, and everyone in the school is worried. Makabe tells everybody his speculation about the trick and gives sarcasm to Kindaichi, yet another student manages to break out the code left by Ruiko as a dying message.

Miyuki gets heavily injured and is sent to hospital because of the attack from the killer and later wakes up. Kindaichi returns to the school in attempt to solve the mystery, therefore calling everybody inside to gather. The seventh mystery was man-made, and one man is said to be the murderer.

A famous writer recently died and according to his will, his inheritance will be divided by his five successors. One of the successors, Takarada invites Hajime, Saki and Miyuki to the Russian Mansion in Hokkaido.