After the events of "Ice Age: The Meltdown", life begins to change for Manny and his friends: Scrat is still on the hunt to hold onto his beloved acorn, while finding a possible romance in a female sabre-toothed squirrel named Scratte. Manny and Ellie, having since become an item, are expecting a baby, which leaves Manny anxious to ensure that everything is perfect for when his baby arrives.

Diego is fed up with being treated like a house-cat and ponders the notion that he is becoming too laid-back. Sid begins to wish for a family of his own, and so steals some dinosaur eggs which leads to Sid ending up in a strange underground world where his herd must rescue him, while dodging dinosaurs and facing danger left and right, and meeting up with a one-eyed weasel known as Buck who hunts dinosaurs intently.