Ellie is expecting, and this makes Manny extremely anxious to create a secure environment for her and their future child, determined to avoid the tragic fate that befell his first wife and child. However, Manny’s intense worry starts to distance him from Diego, who feels compelled to contemplate abandoning the herd as he senses a loss of his primal hunter instincts. Meanwhile, Sid, harboring fears of being left alone, stumbles upon three seemingly abandoned eggs buried underground, which he eagerly decides to adopt as his own. Despite Manny's urging to return the eggs, Sid ignores him and nurtures them, leading to the hatching of baby Tyrannosaurus the next morning.
On a parallel note, Scrat finds himself smitten with a flying saber-tooth squirrel named Scratte, although her sole interest lies in his acorn, taking center stage in his comedic misadventures. As Sid struggles to raise the rambunctious little dinosaurs, their playful antics drive the younger animals away and leave Manny’s carefully constructed playground in ruins, infuriating him. This chaos culminates when the mother Tyrannosaurus arrives, searching for her stolen eggs. When Sid refuses to concede them, she whiskers him and her babies underground.
In a surprising turn of events, Manny, Ellie, and the possums find themselves venturing into a rich, subterranean realm populated by dinosaurs considered extinct. After encountering a menacing dinosaur, they reunite with Diego, only to face an even larger threat. Their fortune changes with the appearance of Buck, a one-eyed weasel who has survived in this jungle for years, on a relentless quest to track down Rudy, an intimidating albino Baryonyx who instills fear among the inhabitants of the lost world. Buck readily agrees to guide Manny and the others toward Lava Falls, where the mother dinosaur has taken Sid and her hatchlings.
As the plot thickens, the mother Tyrannosaurus, initially hostile, begins to soften toward Sid. But when Sid inadvertently finds himself isolated and pursued by Rudy, he narrowly escapes, only to be stranded on a precarious rock drifting toward the fiery rapids of lava falls. The tension escalates when Ellie goes into labor, and a pack of Guanlong triggers a rockslide that separates her from the group. Buck heroically instructs Manny and Diego to guard Ellie, while he takes the possums on a daring mission to rescue Sid. Diego discovers his lost courage in fending off the Guanlong, providing emotional support to Ellie during her childbirth.
In the midst of this chaos, Buck, along with Crash and Eddie, commandeers a Harpactognathus, but they soon find themselves pursued by a pack of Quetzalcoatlus. Utilizing explosive berries, they fight back, leading to a series of hilarious misfortunes, including one Quetzalcoatlus becoming a comically inflated balloon. With the route to Lava Falls cleared, they rush to save Sid just as he teeters on the brink of disaster. Amidst all the mayhem, Manny finally reaches Ellie just in time to witness the birth of their daughter, whom they joyously name “Peaches.”
As they prepare to leave, another encounter with Rudy threatens their safety, but in a twist of fate, the mother Tyrannosaurus takes charge, charging at Rudy and sending him tumbling over a cliff. With heartfelt goodbyes exchanged, Sid bids farewell to the dinosaurs, while Buck contemplates his future now that Rudy is gone. Nevertheless, a throaty roar hints at Rudy's survival, prompting Buck to shield the herd by barricading the path to the lost world.
With a new family member in tow, Manny and Ellie welcome Peaches into their frosty existence, while Diego elects to stay with the herd. Buck, driven by his desire to tame Rudy, opts to remain below. A comedic closing scene unfolds as Scrat and Scratte strive to share their new life in the jungle. However, Scratte's domineering nature leads Scrat to prioritize his beloved acorn once again, setting off a hilarious chain reaction that ultimately finds both Scrat and the acorn bouncing back to the surface, leaving Scrat in exasperation after another mishap.
