In Puzzles For Clef, the player finds himself on an adventure as he takes control of Clef. The action takes place on a sky island in a fantasy world. The main character turns out to be a rabbit named Clef, who receives a letter from her sister Cres and goes on a journey. Based on the letter, she tries to get to the hidden treasures located on the island of her ancestors. She knows these places very well, but as she moves she has to overcome dangers and difficulties. The story is about sisterly love. Two relatives are far away and cannot communicate directly, sending letters and telling them how much they miss them.