As the Alvin and the Chipmunks crew steps aboard a cruise ship en route to the International Music Awards, pandemonium strikes. The tumultuous team, led by Dave Seville, finds it impossible to avoid mischief, leading to the captain summoning Dave to ensure his animated friends stay in line. Unfortunately for Dave, his efforts are short-lived as Theodore, Alvin, Simon, Jeanette, Eleanor, and Brittany soon sneak away to explore the ship’s casino, leaving the anxious Dave behind, with Theodore as the only one who stays put.
Amidst this chaos, an unexpected complication arises: Dave discovers that his former boss, Ian Hawke, is back in action, now disguised as a pelican and serving as the ship's safety supervisor. Ian has his sights set on keeping the Chipmunks and Chipettes under strict surveillance to prevent any further disruptions.
Tensions heighten as Alvin decides to try para-sailing with a kite, but the winds whisk them away, resulting in an adrenaline-fueled chase where Dave must follow with a hang-glider. Ian, driven by his own agenda, attempts to interfere but ultimately finds himself stranded alongside Dave out in the vast Pacific.
Washing ashore on a deserted island, the Chipmunks spend the night while Dave reluctantly partners up with Ian to search for them the next morning. There, they encounter Zoe, a castaway intrigued yet intimidated by their presence.
Settling into Zoe's treehouse brings its share of challenges: Eleanor twists her ankle, and Simon suffers a spider bite, triggering an unexpected transformation into "Simone," a charming French adventurer who is irresistibly drawn to Jeanette. Despite his newfound charisma, "Simone" maintains only a passing interest in Alvin and Brittany.
As they navigate their unfamiliar environment, Zoe leads them to a serene lake adorned with a stunning waterfall, where "Simone" discovers a secret cave and emerges brandishing a glittering gold bracelet, which he presents to Jeanette as a makeshift crown.
However, uncertainty looms when Brittany and Alvin stumble upon an active volcano and express the urgent need to leave the island. Meanwhile, Theodore and "Simone" reunite with Dave and Ian, who are tirelessly crafting a raft for their escape.
As the group searches for food, calamity strikes again when "Simone" gets knocked out and Jeanette is abducted. With Simon back to his original self, he teams up with the others, rallying together to construct a raft and plan their getaway.
Upon waking, Simon's memory of the events leading to his transformation is gone. Soon after, they realize Jeanette has gone missing, pushing the group to the waterfall in pursuit. Alvin and Dave take matters into their own hands, opting to rescue Jeanette while the rest follow closely behind.
Upon reaching a tree log marking their crossing point, they discover that Zoe is using Jeanette to get her hands on treasure hidden deep within the cave. It becomes clear that Zoe had intentionally sought out the island, motivated by treasure, and her ten-year isolation has left her with a fierce resolve to seize it at any cost.
Alvin and Dave jump into action to save Jeanette as the island starts to tremble. When Zoe loosens her grip on the rope holding Jeanette captive, she seizes her chance to escape alongside Alvin and Dave, racing toward their makeshift raft as the ground shakes violently. In a bold maneuver, Alvin uses the Swiss Army knife that Dave previously confiscated to cut the rope.
Once back on the raft, Zoe confronts her actions and apologizes to Jeanette for her earlier wrongdoings. As a gesture of reconciliation, Jeanette gifts Zoe the gold bracelet Simon had earlier presented to her, signifying a shift in their fraught relationship.
In the wake of their adventure, Alvin mends his relationship with Dave, and they are ultimately saved from the island's menacing hold. In a heartwarming conclusion, Ian finds new inspiration as a screenwriter, selling his newly penned script about Zoe's journey to Hollywood, which helps restore both his fortunes and Zoe's notoriety.
As the group boards a plane returning to Los Angeles, Alvin can’t resist pulling one last prank, misleading fellow passengers into believing they are headed for Timbuktu, much to Dave’s chagrin.
