When Nim (Bindi Irwin) and her father Jack (Matthew Lillard) discover that property developers have purchased Nim's Island, Jack heads to the city to convince the powers-that-be that their island must be preserved at all costs. Nim stays behind to prove that a minimum of three endangered species currently live on the island and so the island is legally protected.

Meanwhile, Edmund (Toby Wallace) is hiding out on the island after running away from home. But he's inadvertently brought a new threat with him - a band of pirate animal poachers led by Booker (John Waters). Now, they find themselves in a battle of cunning and wits to free her beloved Sealion Selkie, rescue the animals and save Nim's Island.