Manny, Diego, and Sid join up with Buck to fend off a meteor strike that would destroy the world. Scrat's epic pursuit of his elusive acorn catapults him outside of Earth, where he accidentally sets off a series of cosmic events that transform and threaten the planet. To save themselves from peril, Manny, Sid, Diego, and the rest of the herd leave their home and embark on a quest full of thrills and spills, highs and lows, laughter and adventure while traveling to exotic new lands and encountering a host of colorful new characters.

Manny, Diego, and Sid embark upon another adventure after their continent is set adrift. Using an iceberg as a ship, they encounter sea creatures and battle pirates as they explore a new world. When Scrat accidentally provokes a continental cataclysm with a storm, Manny is separated from Ellie and Peaches on an iceberg with Diego, Sid and Granny but he promises that he will find a way to return home. While crossing the ocean, they are captured by the cruel pirate Captain Gutt and his crew. However they escape and Manny plots a plan to steal Captain Gutt's ship and return to his homeland in a dangerous voyage through the sea. But the cruel pirates seek revenge against Manny and his family and friends.

When Sid's attempt to adopt three dinosaur eggs gets him abducted by their real mother to an underground lost world, his friends attempt to rescue him. 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.