1951. More than anything twelve-year-old Hannah Heywood wants to attend a “normal” school. She grabs the opportunity of her family's move to Spyder Hill, Texas, to take control of her life. Enrolling herself in the local junior high school, she gets on the swim team and begins to teach herself the basic arithmetic she failed to learn back in Virginia at what she calls a “special school for misfits”.
Informed by her Uncle Andrew, former P-51 fighter squadron commander with two silver stars, Hannah “meets” the woman pilot Amelia Earhart who becomes her best friend and confidante. Through imaginary conversations and adventures with Amelia, Hannah develops the ability to trust and to learn common sense.
Hannah's journey with Amelia occurs in the context of a family that is bubbling with unresolved conflict. Uncle Andrew, marked by the horrors of the dropping of the atom bomb on Japan and now turned Presbyterian minister, is full of zeal to urge pacifism on his reluctant congregation. When his former lover Yosano of Occupied Japan dies of leukemia from radiation exposure, his zeal turns to obsession. Hannah's mother struggles with the aftermath of her husband going missing in action in the recent war. Hannah's sister, Cynthia, jerked out of the senior year of a private high school and thrown into the small public school in Spyder Hill, has to face all the insecurities and stress of making a new place for herself.
All the while Hannah is pursuing the mystery of the lost B.J. Nealson, a girl Hannah's own age who disappeared from Spyder Hill only months before Hannah's arrival. Everyone believes the alleged Nazi Gunther Van Heusen is the culprit, but conclusive evidence has not been found. Hannah swims through the swirl of events and emotions, oblivious that BJ's real killer is watching her closely as she moves nearer and nearer the truth about the girl's disappearance.