Ellie and Manny, the two woolly mammoths, are expecting their first child, and Manny struggles to make life perfect and safe for the family. At the same time, Diego the saber-toothed cat decides to leave the herd because he thinks he's losing his edge and isn't meant for the family life. Sid the ground sloth begins to wish for a family of his own and takes three apparently abandoned eggs that he finds in an icy cavern and calls them Egbert, Shelly, and Yoko. Manny tells him to put them back, but Sid ignores Manny and looks after the eggs, which hatch into baby Tyrannosaurus rex the next morning. Meanwhile, Scrat encounters a female saber-tooth squirrel Scratte and battles with her for the acorn he desperately wants.
Although Sid tries his best to raise the three dinosaurs, their rambunctious behavior scares away all the younger animals and ruins a playground Manny built for his child. Not long after, a female Tyrannosaurus rex, whose eggs Sid stole, returns and carries both Sid and her young underground, with Diego in pursuit. Manny, Ellie, Crash and Eddie the opossums follow as well and discover that the icy cavern leads to a vast subterranean jungle populated by dinosaurs thought to be extinct. Here, an angry Ankylosaurus threatens The Herd despite Diego's efforts to fend it off. Then they are saved from a further crowd of angry reptiles by a deranged, quick witted, one-eyed weasel named Buck.
Buck has been living in this jungle for quite some time and is fighting Rudy, a huge albino Baryonyx, intending to avenge the eye he lost to it when he was young with a knife he carved from one of Rudy's teeth. He agrees to lead The Herd through the jungle's perils to Lava Falls, where the dinosaur has taken Sid and her babies. In the meantime, Sid and the mother T-Rex try to outdo each other in feeding the offspring; he loses this contest, but is welcomed into the family regardless. The next day, however, Sid is separated from the family and attacked by Rudy. Sid is knocked onto a loose rock slab that is floating on a river of lava and about to plummet over the falls.
As The Herd moves toward Lava Falls, Ellie goes into labor and a Guanlong pack strikes, causing a rock slide that separates her from Manny and Diego. Manny doubles back to protect her and Diego fends off further attacks, while Buck takes Crash and Eddie ahead to rescue Sid. Just as he goes over the falls, the trio swoops in on a commandeered Harpactognathus only to be chased by a flock of Pterodactylus on the way and saves his life. Manny reaches Ellie just in time to hear the cry of a newborn baby girl. Manny initially wants to name the baby “Ellie” after her mother but Ellie suggests the name Peaches after the fruit and the code name her and Manny agreed to use to signal when the baby is coming. Sid is saddened at the fact that he never had a chance to say goodbye to "his" children as he returns to The Herd and learns of Peaches' birth.
Before they can leave the jungle, they are ambushed by Rudy, who begins to attack them at full force. Working together Manny, Sid, Diego, and Buck manage to trap Rudy by ensnaring him in vines. However, he quickly breaks free and resumes his onslaught. The Herd is saved by the timely arrival of the mother T-Rex, who charges at Rudy and knocks him off a cliff. As she and her children wish Sid well, Buck, now without a purpose in life since Rudy is gone, decides to join The Herd and live on the surface. However, a distant roar tells him that Rudy is still alive. Because of this he changes his mind and sends The Herd home, blocking off the path to the underground jungle at the same time. Manny and Ellie welcome Peaches into their frozen world and Manny admits to Sid that he did a good job looking after Momma's children. Diego decides to remain with The Herd, while Buck stays underground, happily battling it out with Rudy and riding him.
Meanwhile, Scrat and Scratte, who had fallen in love with one another, decide to stay down in the jungle together. Unfortunately, Scrat's greed for his precious acorn overcomes his newfound romance with Scratte, and he ultimately chooses the acorn over her. Subsequently, Scratte and Scrat battle once more for the acorn, resulting in Scrat being repelled to the surface while Scratte is left trapped in the jungle. Scrat celebrates with his acorn, however, once again, loses it, much to his frustration.
