The Innocents follows two girls, Jane and Maggie, who form an unlikely friendship in a small Indiana town during the summer of 1961. The girls investigate an old attic where they uncover a diary of Jane's mother's telling of her illicit love for a young black man in the 1940's.

Jane and Maggie quickly become best friends, but reading about her mother's mysterious past leads Jane to question her own. So when Jane finds out she'll be leaving soon to attend Radcliffe University, and following an abusive incident involving Maggie and her father, the girls decide to go on a road trip in search of answers to her mother's past.

Along their journey, the girls discover more about their pasts then they first expected while finding in each other their first true friend on an adventure that will forever change their lives and the way they see the world.

When they reach their destination, a young black naval officer, James, introduces himself as Jane's brother from their mother's early affair. The girls stay up through the night with James trying to piece together the mysteries of their pasts.

In the morning, the girls say goodbye to James and hop a freight train back to Brownsville for Jane to catch her train to Radcliffe. With her best friend leaving for college, Maggie decides not to stay with her abusive father on a farm that no longer holds any future for her. Maggie packs her bag, says a tearful farewell to her sleeping father and meets Jane at the train station. After a sad farewell, both leave Brownsville, Indiana for their promising new futures.