Moose Flanagan and his family move from Santa Monica to Alcatraz Island in the 1930s. The move was caused by the father's new job positions as an electrician and as a guard in the well known Alcatraz prison. Off the island there is a very prestigious school for children with mental illness called the Esther P. Marinoff School. While she could not be diagnosed at the time, Moose's sister, Natalie, is explained by the author as being autistic. She is fifteen years old during most of the book, but Mrs. Flanagan tell people that Natalie is ten so that they will not believe she is too old to be helped. Mrs. Flanagan tries applying Natalie to the Esther P. Marinoff School.
Mrs. Flanagan believes this is the only way to help "cure" Natalie of her peculiarity and is doing her best to avoid sending Natalie to a mental institution. Due to his parents' hectic work schedule Moose is left with almost full responsibility of his autistic older sister Natalie along with fitting into his new school. Natalie is accepted into the Esther P. Marinoff School, but unfortunately, she's sent back home almost immediately because she's just not adjusting to the school. Moose's mother and Natalie's new psychologist, Mrs. Kelly, push Moose to take full care of Natalie and to take her everywhere he goes to help improve her social skills.
Moose becomes friends with the warden's daughter, who talks him into being part of her money making scheme. One of her schemes is a criminal laundry service for the kids at school. Once the scheme flops and the Warden hears of it, the children are punished and have to find a new hobby. Moose decides to hang around the prisoners' rec center trying to find a stray baseball just to help him fit in with the other kids on the island. Moose eventually notices his older sister Natalie developing a relationship with convict 105, also known as Onion.
The convict knows Moose has been looking for a baseball, and he hands Moose a ball just for amusement. Moose becomes scared for his autistic older sister until he realizes the relationship will be ending soon because his sister's second interview with Esther P. Marinoff School is coming up soon. Moose and his family's hopes are crushed when the school rejects Natalie. Out of ideas, Moose decides to take a risk with the help of Piper and writes a letter to the infamous criminal Al Capone, asking him to pull any strings he has to help Moose's family get his sister back into school. Within days, Natalie is accepted into the new branch of Esther P. Marinoff School for older children. The next day Moose is getting ready for the day when he finds a note in the sleeve of his shirt with the word "done" underlined.