Four years after the exhilarating journey at the Earth's core, Sean Anderson is already embroiled in another adventure. His latest escapade culminates with a high-speed dirt bike chase that ends dramatically in the pool of Mr. and Mrs. McGuillicutty, much to the dismay of the authorities pursuing him. His stepfather, Hank Parsons, shows up to mitigate the situation, only to learn from Officer Jim that Sean's reckless actions included a daring break-in at a satellite control facility—an act that could have landed him in serious trouble, had the McGuillicutty's not opted to forgive him.
Back at home, Sean faces a reprimand from his mother, Liz, who expresses her disappointment over his reckless behavior, while Hank is left contemplating Sean's motivations. When he discovers that Sean's antics stemmed from a desire to enhance a coded signal linked to his missing grandfather, Alexander, he decides to get involved.
Together, Sean and Hank work tirelessly to decode the signal, which transports them through three classic novels: Treasure Island, Gulliver's Travels, and Jules Verne's Mysterious Island. Using maps inspired by these texts, Hank creatively overlaps them to suggest a singular island's coordinates. Though his original intention is to prove to Sean that no hidden island exists, Hank ultimately hopes to create a stronger bond with him.
Convincing Liz to let them embark on this intriguing journey, Hank hires helicopter pilot Gabato and his daughter, Kailani, who catches Sean's eye, to fly them to the defined coordinates. However, their adventure veers off course when they become trapped in a cyclone and crash into the Pacific Ocean.
Upon regaining consciousness on the island, they are greeted by a fantastical environment where animals of unusual sizes roam—think compact elephants and enormous butterflies. The trio soon encounters a dangerous prehistoric creature: a dwarf Sicilian elephant, and in a chaotic twist of fate, Gabato inadvertently rouses a colossal frilled lizard, sending the group into a panicked escape.
Just as despair sets in, Sean's grandfather, Alexander, unexpectedly appears, guiding them to a modest hut he built from discarded parts of his ship. With a working radio at hand, their mission becomes clear: they must emit a distress signal, all while dealing with a frustrating two-week wait dictated by the satellite's orbit.
As dawn breaks over the legendary city of Atlantis, its inhabitants confront the grim truth: they have little time to escape an imminent disaster. This island, which resurfaces only every 70 years, has already begun to sink back into the sea. Alexander’s reassurances of having ample time are met with skepticism as Hank notices a troubling surge of seawater bubbling from beneath their feet. Their survival now hinges on the enduring Nautilus—the fabled submarine of Captain Nemo, as hinted in a cryptic journal that leads Kailani to the entrance of Poseidon's Cliffs.
Their journey towards this underwater sanctuary becomes uniquely adventurous as they ride giant bees, navigating perilous heights. In a pivotal moment, Sean demonstrates his quick reflexes by saving Kailani from a deadly attack, an act that leaves him with a dislocated ankle. Luckily, Hank and Alexander quickly come to his aid, and Hank lightens the mood with a heartfelt rendition of ">What a Wonderful World," strengthening their camaraderie.
When morning arrives, they face the harsh truth: the island will soon drown, with only hours left to find safety. Gabato’s reckless treasure pursuit leads him into a dangerous situation within the volcano, threatening their collective survival. As Alexander and Kailani race to retrieve him, Sean and Hank seize the chance to head toward Poseidon's Cliffs, determined to escape the unfolding catastrophe.
To access Nautilus' underwater refuge, they fashion makeshift oxygen tanks and plunge into the ocean's depths, where a terrifying encounter with a massive electric eel-moray hybrid nearly proves fatal. Through quick thinking, they manage to use the creature's energy to revive the submarine's long-dormant batteries.
Meanwhile, Kailani and Alexander successfully pull Gabato away from his reckless treasure hunt as the volcano erupts in a stunning explosion. Just in time, Sean and Hank rescue their companions, with Gabato skillfully piloting Nautilus to safety as they fend off collapsing debris with torpedoes. Amid the chaos, Kailani acknowledges Sean's bravery with a tender kiss, sealing their bond.
Fast forward six months later, as Palau thrives with tourists eager to dive into the ocean's mysteries aboard Nautilus, Kailani and Gabato have established a successful business. On Sean's birthday, Kailani pays him a visit, only to be joined moments later by Alexander, who presents him with a thoughtful gift—Jules Verne's From the Earth to the Moon, an exciting invitation to set forth on their next great adventure, despite his mother Liz's reservations.
