High school student Kindaichi Hajime "Yamada Ryosuke" solves a variety of difficult cases that he gets entangled in with the deductive powers inherited from his grandfather, the famous detective Kindaichi Kosuke.

Story continues with the students' own conflicts, Koro Sensei’s identity and the fate of the world. The time limit for assassination is approaching.

In 2012, Atsuya (Ryosuke Yamada) and his 2 childhood friends do something bad and run into an old general store. They decide to stay there until the morning. Late into the night, Atsuya sees a letter in the mailbox. The letter is addressed to the Namiya General Store and the letter was written by someone to consult about worries. Incredibly, the letter was written 32 years ago. The mailbox is somehow connected to the year 1980. Atsuya and his friends decide to write a reply and place their letter in the mailbox.

Two alchemist brothers go on a quest for the Philosopher's Stone after an attempt to revive their dead mother goes horribly wrong.