Professor Layton and his assistant Luke go to the small village of Saint-Mystère at the request of Dahlia Reinhold, second wife of the late Baron Reinhold, who wants their help in solving an enigma left by her late husband. The Baron had written in his will that whoever found the Golden Apple, hidden in the village, would inherit his entire fortune.

The two investigators reach the outskirts of the town and quickly notice that the majority of the inhabitants are passionate about riddles and puzzles of all kinds, of which the professor and the young boy are also keen. They can also see in the distance a mysterious tower located in the center of the village...