Suzy returns with her parents and is forbidden from seeing Sam again. Sam stays with police Captain Sharp (Bruce Willis) while they await Social Services (Tilda Swinton), who will place him in a "juvenile refuge" because his foster parents no longer wish to house him. The Scouts, who previously were not kind to Sam, later decide it is their duty to help the young lovers run away again. Suzy, Sam, and the other Scouts seek out the help of Cousin Ben (Jason Schwartzman), an older relative of one of the Scouts who works at the larger Khaki Scout summer camp, Fort Lebanon, run by Commander Pierce. After many twists and turns, Sam and Suzy eventually are apprehended on a church steeple during a violent hurricane and flash flood, evoking the earlier references to Noah. The church steeple is destroyed by lightning, but everyone survives.
Sharp decides to become Sam's legal guardian, saving him from the orphanage and allowing him to remain on the island and be with Suzy. The last scene takes place at Summer's End, with Sam painting a landscape of the cove and then slipping out the window as Suzy and her brothers are called to dinner.