In the summer of 1965 on the New England island of New Penzance, a place untouched by time, twelve-year-old orphan Sam Shakusky, equipped with wilderness survival skills and a penchant for adventure, quietly escapes from his Khaki Scout camp. Unbeknownst to the scout master and other scouts, Sam has orchestrated an elaborate plan to meet up with his pen pal and kindred spirit, Suzy Bishop. Suzy, an intelligent and misunderstood girl with a love for fantasy books, longs to escape the confinement of her life and the misunderstandings of her family. Together, the pair of young misfits commit to running away, armed with Sam's camping equipment and Suzy's stolen library books, her brother's battery-powered record player, and her cat.

Their disappearance quickly sparks a search that grips the island community. The pursuit involves the sad and lonely local police captain, an overzealous scout master, the rest of the Scout troop, and Suzy's quirky parents. All are profoundly affected by the children's quest for freedom and a place of their own, away from the judgment and expectations of the adult world. As a violent storm approaches the coast, stakes and tensions rise. Islands' search parties scour the land for the runaways, who are testing their survival skills and the strength of their burgeoning love against the wilderness of the island and the inevitable confrontation with their pursuers.