The film concludes with a convergence of all plot lines during a massive hurricane.
- The Climax: Sam and Suzy are cornered on the roof of the church, which serves as a storm shelter. Social Services arrives to take Sam to a juvenile refuge (an orphanage). To escape, Sam and Suzy climb the steeple during the lightning storm, prepared to jump together rather than be separated.
- The Resolution: Captain Sharp intervenes, not as a police officer but as a protector. He offers to legally adopt Sam, saving him from the orphanage. The steeple is struck by lightning, leaving the three dangling, but they are pulled to safety.
- The Ending: In the aftermath, balance is restored. The Bishop parents stop their imminent divorce. Captain Sharp and Sam live together happily. Sam and Suzy are still together, though they now meet secretly with the tacit approval of the adults.
- Final Image: The film ends with a shot of Sam's painting of the cove, now titled "Moonrise Kingdom," dissolving into the real landscape. This reveals that while the physical storm washed away their campsite, the memory and the emotional reality of their kingdom remain immortalized in art.