It has been four years since the events of the first movie. Seventeen-year-old Sean Anderson (Josh Hutcherson) is caught by the police after a brief chase on his dirtbike which ended with him driving into a swimming pool while trying to evade them. Minutes later, his stepfather Hank (Dwayne Johnson) arrives where a police officer (Stephen Caudill) who is friends with Hank tells him that Sean has illegally broken into a remote satellite research center, and that he has talked Mr. and Mrs. McGillicutty (the owners of the swimming pool) out of pressing charges. Hank takes Sean home where his mother Elizabeth (Kristin Davis) is not pleased with his actions and/or the fact that he and Hank don’t get along well.
Hank discovers that Sean trespassed the satellite research center in order to boost the signal of a code Sean received from someone he suspects is Alexander Anderson, Sean’s grandfather who had been missing for two years. Wanting to bond with his stepson the next day, Hank helps Sean decipher the code of Jules Verne characters which lead to three books: Treasure Island, Gulliver’s Travels, and Verne’s own Mysterious Island. Using the books’ individual island maps, Hank suspects they are books of the same island and uses a back light in order to make them all one completed land mass with the coordinates to its location. Hank manages to convince Liz to let both of them go in search of the island, in slight hopes of proving Sean wrong, that there is no so-called mysterious island there.
They arrive in Palau where they need transportation to travel to this dangerous part of the ocean. A Palauan helicopter tourism guide Gabato (Luis Guzman) and his daughter Mackenzy (Vanessa Hudgens) who Sean develops an immediate crush on, agree to fly them out to the island for $3,000, but the helicopter gets caught in a category 5 hurricane and they crash into the Pacific, waking up on the island.
Crossing into the island, they discover one of the laws of the Mysterious Island is that, all animals big are small and all animals small are big (inspiring Lilliput from Gulliver’s Travels). The crew discover tiny elephants and giant butterflies, which are the first creatures they come across on the island. The group decides to explore further into the island.
After leaving that part of the island they come across an egg clutch belonging to a Giant Frilled Lizard, they are then saved by Sean’s grandfather Alexander (Michael Caine) who takes them to a large hut he’d built from the wreckage of the ship that brought him to the island called the Blue-Eyed Lucy. He has a working radio, but due to the positioning of the communications satellite it would be two weeks before they could call for help.