On Jack's tenth birthday, Madeleine repeats the three rules before taking him into town for the first time. He meets a girl in town named Acacia and become infatuated with her. After starting school shortly afterward, he also meets Joe, a bully who is in love with Acacia as well.
Jealous, the older boy and his gang of students torment Jack for the next four years. During an assult from Joe, the cuckoo of Jack's clock heart gouges Joe's eye, and Jack runs home believing he had murdered Joe. Madeleine, believing Jack to be a fugitive, helps him escape. Jack only wants to see Acacia again and eventually meets up with Georges Melies, a magician attempting to operate an early film camera. Georges helps repair his heart and agrees to join Jack in search for Acacia. They proceed to Andalusia, Spain, the country she was born in, in search of her. After a long journey they arrive at a circus in Andalusia. Jack finds Acacia but Georges advises him against revealing his identity to her. He proceeds to befriend her and fooloshly avoids sharing his feelings. She hints that her heart belongs to somone from her past. Jack eventually finds a way to reveal himself and gives a key to Acacia which can be used to wind his heart.
Soon after Joe, the bully from Jack's past, shows up. He had been looking for an opportunity to futher punish Jack and explains to her the three rules of Jack's cuckoo clock heart in an attempt to sabotage them. Acacia, after taking with Joe, decides she doesn't want to risk being the cause of death of Jack by allowing him to fall in love. She rejects him, and leaves with Joe. Acacia eventually realizes she holds the key to Jack's survival and returns to search for him. She finds out quickly that Jack had departed for home in Edinburgh and follows behind him. She knows she only has a short time to reach him. She does, but he throws away the key, choosing love over life. Then they finally kiss, time stops, and he dies.