During a game of hide-and-seek, Otto pauses to read a storybook about three lost princesses named Eins, Zwei and Drei, who are cast out by their father and raised by a witch in the forest. Otto gets lost in the woods. He trips and falls, knocking himself unconscious. When he wakes up, he finds himself with Eins, Zwei and Drei, who ask him to read them their own story.
In the story, the three sisters grow up doing household chores for the witch, who is indifferent to them. The sisters have magically beautiful voices, and they long to escape the witch’s cottage and have a happy family life. As the years pass, the old king dies, and the new king, the girls’ younger brother, learns of his three older sisters’ existence and invites them to his coronation.
The witch is angry that the sisters want to leave, so she curses them. They must remain in the forest unless two conditions are fulfilled. First, their spirits must enter a woodwind instrument to be carried away from the forest; second, they must save a soul about to die.
Otto stops reading the book because the pages end, and he tries to help the girls escape. He offers them his new harmonica. Each sister plays a short tune, which places her spirit inside the harmonica. The girls tell him that his fate will always tie him to the people who have played the harmonica before him and those who will play it afterward.
Otto wakes up the next morning, alone in the forest with no book. When he plays the harmonica, he feels his name being called and a path through the forest opening for him. The path leads him directly to a search party that is looking for him.
Although he tells his parents about the three sisters and the harmonica, they insist that the harmonica is not magical. As time goes by, Otto grows up and stops telling the story of the sisters, though he occasionally plays the harmonica when he feels afraid.
In 1933, in Trossingen, Germany, Friedrich Schmidt is a shy 12-year-old boy with a striking purple birthmark covering half his face. Adolf Hitler is the new chancellor of Germany, and Friedrich’s father despises Hitler’s increasingly narrow-minded laws and policies. Friedrich doesn’t attend school with other children. Instead, he works with his Uncle Gunter in a harmonica factory.
One day he hears a haunting melody coming from an abandoned warehouse next to the factory. In the warehouse, he discovers a harmonica that looks very old. He takes it home. As he plays it, he realizes that its music is more beautiful than any other harmonica he has played and that he feels braver. The harmonica is marked with a painted red letter “M,” distinguishing it from other harmonicas.
Friedrich is troubled when his older sister, Elisabeth, returns home from nursing school and reveals that she supports Hitler and his policies for creating a racially pure Germany. Elisabeth warns their father that because of Friedrich’s birthmark and his childhood bout of epilepsy, he will have to receive a sterilization surgery to ensure that he cannot pass on his genetic deformities to the next generation.
The situation in Trossingen worsens until Mr. Schmidt and Uncle Gunter realize they must leave Germany entirely. Before they can leave, Mr. Schmidt is taken into custody by the police and sent to a hard-labor camp in Dachau for being sympathetic to Jews and harboring anti-Nazi views. Friedrich prepares to travel to Dachau with a bribe so the camp will release his father, but he knows he must leave his beloved harmonica behind him or it will be confiscated when the guards search him.
In 1935 in Pennsylvania, 11-year-old piano prodigy Mike Flannery lives in the Bishop’s Home for Friendless and Destitute Children. His younger brother, Frankie, is only 7. Since their grandmother’s death, Mike is the only support system Frankie has.
A miracle seems to occur when a lawyer named Mr. Howard, representing the estate of a wealthy woman named Mrs. Sturbridge, says he needs to adopt a musically talented child on his client’s behalf, but is willing to take two. Mike and Frankie go to live at Mrs. Sturbridge’s mansion and are well-fed and well-treated by the staff, although they rarely see Mrs. Sturbridge herself.
Mike learns from Mr. Howard that Mrs. Sturbridge used to be a concert pianist, but she stopped playing after her only son’s death and her subsequent divorce from her husband. Mrs. Sturbridge’s late father wanted her to enjoy family life again, so he specified in his will that his daughter must adopt a child within one year of her father’s death or be left penniless.
Mike is devastated to know that Mrs. Sturbridge never wanted to adopt them in the first place and is actively looking for ways to legally reverse the adoption process. He begs Mrs. Sturbridge to at least care for Frankie, insisting that he can find his own way in the world. Mike intends to audition for Hoxie’s Harmonica Wizards, a traveling harmonica band of boys who are internationally famous. If he joins the group, he’ll have food and lodging until he’s old enough to find a permanent job.
Mrs. Sturbridge agrees to help Mike and gives him advice for polishing up his audition. Mr. Howard buys him a harmonica with a mysteriously musical quality, which has a red letter M painted on it. Mike makes it to the final auditions but decides to run away from home with Frankie when he learns that Mrs. Sturbridge has betrayed him by obtaining the paperwork to reverse Frankie’s adoption, as well as his own.
In 1942 in Southern California, Ivy Lopez’s parents are migrant farmers who wish she would think practically about her schoolwork, although her greatest love in life is music. Her older brother, Fernando, has joined the United States Army, and Ivy’s parents eagerly await letters from him. Ivy is crushed when a permanent farming position opens up, and she and her parents have to move to a new town immediately. Ivy takes her harmonica, a special one with the letter M painted on one corner, with her to her new city.
There are tensions in Ivy’s new town. The farm that Ivy lives on originally belonged to a Japanese family called the Yamamotos, who were removed from their home and confined in a camp by the U.S. government. When Ivy starts school, she’s surprised to learn that she’s not attending the Lincoln Main elementary school with her white friend, Susan, but Lincoln Annex, an Americanization school for children who are not considered citizens. The second school is inferior in every respect, and Ivy learns that her only opportunity to study at Lincoln Main will be after school hours, and only if she becomes a member of the elementary orchestra.
A neighbor, Mr. Ward, demands to search the extra buildings on the Yamamotos’ property because he believes they were spies. However, a thorough search only reveals a large collection of musical instruments belonging to Japanese friends of the Yamamotos who wanted to preserve their precious instruments before departing for internment camps. When Kenny Yamamoto, the grown son of the Yamamotos who is an interpreter with the Army, comes to visit the farm, Ivy feels compelled to give him her “M” harmonica.
In New York’s Carnegie Hall in 1951, Friedrich Schmidt is the conductor for the Empire Philharmonic Orchestra. He ushers his father and his Uncle Gunter to their seats before the performance. At the same venue, an adult Mike welcomes Frankie, Mrs. Sturbridge and Mr. Howard to watch him play the piano with the orchestra. Mike had been wrong about Mrs. Sturbridge not wanting to adopt him and Frankie. She married Mr. Howard, and the four of them became a happy family.
Ivy is also part of the concert as a flutist, distinguished by being the youngest member of the orchestra. Her old family friend Kenny Yamamoto is in the audience watching her. When she gave him the magic harmonica all those years ago, he returned to the action of World War II with the harmonica in his chest pocket. The harmonica stopped a bullet that would have killed him.
As he convalesced in the hospital, he saw a vision of three lost princesses tending to him because he was the soul on the brink of death that they were meant to save. Ivy plays beautifully in the concert, unaware of her connection to Friedrich and Mike, all of whom owned the same harmonica.
In a final chapter, the reader learns that the boy Otto grew up to become a famous harmonica maker and that he painted the red letter M on the magical harmonica and sent it out into the world, which allowed Friedrich, then Mike, then Ivy, then Kenny, to receive it.
Once the three princesses saved Kenny, the spell was broken, and they returned to their own timeline and lived happily ever after with their mother and brother in their castle.