Ever since his mother died in an accident, Ben has been plagued by nightmares. Wolves chase him in his dreams and cause him to cry out in his sleep. One night as Ben lies awake, three months after his mother died, he overhears his aunt and uncle arguing about whether to sell his mother’s house because money is tight.
In an effort to calm his nerves, Ben takes out his special keepsake box, a Christmas gift from his mom. Ben uses it to hold the ordinary and unique objects he has collected over the years: His last baby tooth, a few twigs, a plastic game piece. All are displayed within small cubbies inside the box.
As Ben looks out his bedroom window, he is shocked to see a light on in his old house, which is less than 100 feet away from his aunt and uncle’s house. He slips out of bed and finds his cousin Janet, wearing his mother’s clothes, smoking her cigarettes and dancing to one of his mother’s favorite songs. Janet shows him a can full of money that his mother had kept hidden in her closet. She replaces it, the cigarettes and his mother’s clothes.
Then she urges Ben to return to her parents’ home with her before a storm comes in. Ben chooses to stay in his house. Once Janet leaves, Ben finds an old book titled Wonderstruck. The book was published by the Natural History Museum in New York City and describes what a museum is and the job of a museum curator.
As Ben flips through the pages, he finds a bookmark for Kincaid’s Bookstore. On the back is a note for his mother from someone named Danny, and it includes his phone number and address. Ben wonders if Danny is his father. He examines his mother’s locket and wonders if the picture inside is of his father. The name Daniel is printed on the back.
Ben hides the locket under his shirt. As a thunderstorm breaks overhead, Ben picks up the phone to call the number on the bookmark. Lightning strikes the house, passes through the phone and renders Ben unconscious.
Interspersed with the written story of Ben is another story about a lonely, tween girl. Her story is told through beautiful pencil sketches. She climbs out a window of her house and hurries to a nearby river to send a paper boat afloat with the words “Help me” written on it.
Then she runs away to the cinema to see her favorite actress, Lillian Mayhew, in her newest silent picture. Afterward, the girl returns to her home. In her room, she has built a model of a city out of paper. She sees a new book on her bed, left by her tutor. It is a manual to teach deaf people how to lip-read and speak. The girl rips out the pages and creates another building.
At the dinner table, her father is angry when he discovers she has cut a story from his newspaper. He sends her back to her room. The girl reads the story about how Lillian Mayhew is going to star in a Broadway show. The girl packs a suitcase, including a postcard from someone named Walter. We learn from the card that the girl’s name is Rose. Rose sets off for New York City.
In Part Two of the book, Ben also makes his way to New York City. The electrical shock that rendered him unconscious also made him deaf. While undergoing tests in Duluth, Ben asks his cousin Janet to bring him some clothes from home and the money can. He uses the funds to buy a bus ticket, hoping to find his father. When he arrives, he pulls his money out of his pocket so he can buy a hot dog and is robbed.
Ben finds the address written on the back of the bookmark, but no one named Danny lives in the building. He then discovers that the bookstore on the bookmark is a vacant building. A boy tries to talk to Ben, but afraid and upset, Ben runs away. He heads toward the Museum of Natural History.
As he hurries up the stairs, he trips on the top of the stairs and his suitcase falls open, spilling his belongings, including his special box. The boy who had seen him at the bookstore hands him back the book, Wonderstruck. Ben puts it in his suitcase, then runs into the museum.
Rose finds the theater where Lillian Mayhew is rehearsing her play. Lillian is angry when she discovers Rose hiding in the wings, watching her. Through notes, the reader learns that Lillian is Rose’s mother. Rose begs to be allowed to live in the city with her mother, but Lillian refuses. It is too dangerous of a place for a deaf girl.
Lillian locks Rose in her dressing room, while she goes back to the rehearsal. Rose escapes through a window. She heads toward the building on her postcard, the Museum of Natural History. Eventually, she finds Walter, her brother. Walter takes her home to his apartment.
After cleaning up in the museum’s bathroom, Ben does some exploring. He finds a strange note asking what is inside his box. Looking in his suitcase, Ben discovers his treasure box is missing. The note has a map of the museum drawn on it with an X marked at the end of dotted line.
Ben follows the map to a room with dioramas in it. One of the dioramas is of the wolves of Gunflint Lake, Minnesota, Ben’s hometown. He finds the boy who was at the abandoned bookstore. Through gestures, the boy explains he picked the wolf diorama as a meeting place because Ben’s box has wolves engraved on the top. The boy pulls Ben away from the room, but not before they see an old woman enter and stare at the wolf diorama.
The boy pulls out a tiny notebook from his pocket and communicates with Ben through notes. He explains his name is Jamie and that his father works at the museum. He takes Ben to his secret hiding a place, an old room that is now used as a storage closet. Jamie shares some food with Ben.
When Jamie presses him, Ben reluctantly shows him the contents of his treasure box. He is pleased when Jamie seems enthusiastic and curious about all of Ben’s odd treasures. Jamie leaves Ben for the afternoon as he has somewhere to go with his father. When he returns, Jaime brings more food. The boys spend the evening poking around the museum. Ben asks his new friend to call his aunt and uncle to come to New York and get him.
Ben spends the following day exploring old file cabinets in a deserted hallway of the museum. He eventually finds a file about the wolf diorama. He finds pencil sketches of the lake near his home and the wolves that live there. He also finds a picture of the cabin that his family owned.
A handwritten note mentions meeting someone at Kincaid’s Bookstore. He takes the file back to the storage room to read more. He finds a letter from Daniel Lobel, the exhibition preparator, addressed to Ben’s mother, asking for her help as he works on the wolf diorama. Ben rushes to the information desk and asks to see Daniel Lobel.
He cannot read the woman’s lips, but eventually he figures out that Daniel no longer works there. Ben returns to the storage room, dejected, but then realizes that the storage room had once been an integral part of the museum and that the book Wonderstruck contains a detailed picture of its contents.
Jamie returns the following day with a present for Ben. It is a book about sign language. While leafing through it, Ben finds a bookmark for Kincaid’s Bookstore and realizes the store still exists, but is in a new location. He is angry at Jamie for not telling him. Jamie explains that Ben is the first friend he has made in a long time, and he worries that he will lose touch with him if Ben finds his father or goes home to Minnesota. Ben takes the bookmark and leaves to find the bookstore.
In Part Three of the book, Ben finds Kincaid’s Bookstore. An old woman enters and he recognizes her as the woman who stood in front of the wolf diorama at the museum. The woman greets a salesclerk. They do not speak, but gesture to each other with their hands. Ben falls down the stairs, causing his mother’s locket to open.
The old woman stares in wonder and confusion. Through notes, Ben learns that her name is Rose, and she is Daniel’s mother, his grandmother. She is the same Rose who came to the city as a girl, and the salesclerk is her brother, Walter. She gave the book Wonderstruck to her son as a gift and he, in turn, had given it to Ben’s mother.
Rose takes Ben to the Queen’s Museum of Art and a huge model of the city. She tells Ben about how her brother took her in as a young girl and helped her find a school for the deaf. She met her future husband there and later got a job with the Natural History Museum making models.
When her son, Daniel, was born, she was thrilled to take him to work. He learned to love the museum as well and got a job there. Rose was asked to help create the model of New York City for the World’s Fair exhibit in Queens. The model was so popular that after the fair ended, they kept it and asked her to maintain it. Daniel was asked to create the wolf diorama and went to Minnesota to do research. There he met and fell in love with Ben’s mother. Daniel returned to New York City, where he died a few years later from a heart ailment.
At that point, Rose tells Ben a secret. Within the model of New York City, she has hidden different objects related to her son. A photograph of the day he was born is in the model of the hospital. One of his pencils is in the model of his school. Rose explains that she met Ben once before, when he was very young. His mother had brought him to his father’s funeral.
She did not say that Ben was Daniel’s son, but Rose had seen the resemblance. Rose had hoped to meet Ben again and find out for sure. Ben realizes that he dreamt about wolves because he had seen them before at his father’s funeral. Perhaps it was his father’s way of leading him to his grandmother.
Rose tells Ben that she knows his parents would have been proud of how brave he had been to make the trip to New York. Ben knows he will have to return to Gunflint Lake, but hopes his aunt and uncle will let him visit the city and his grandmother, as well as his friend Jamie, again.