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Scrat's (Chris Wedge) goal for storing his acorn triggers the break-up of the Pangaea landmass into the seven continents we know today by falling in to the Earth's inner core. The Earth's inner core is solid and stationery. Scrat starts chasing his acorn around, which also starts moving the inner core, which causes all the continent to break and separate. The spinning core then throws Scrat back out to the surface of the planet. Scrat lands on a floating ice shelf, which breaks and again separates him from the acorn.

Manny (Ray Romano) and his wife Ellie (Queen Latifah) deal with their teenage daughter Peaches (Keke Palmer). Crash (Seann William Scott) and Eddie (Josh Peck) are now responsible uncles to Peaches. However, while Ellie supports and accepts her daughter's desire to explore and meet new people, Manny is overprotective, irritating Peaches and driving a wedge between the two.

Sid (John Leguizamo) reunites with his family, who abandon him again, with his annoying Granny (Wanda Sykes). Sid's family includes father Milton (Alan Tudyk), mother Eunice (Joy Behar), brother Marshall (Ben Gleib) and Uncle Fungus (Eddie "Piolín" Sotelo).

Manny then catches Peaches hanging out with a group of teenage mammoths he does not approve of and forbids her from meeting them again. Peaches has a crush on Ethan (Drake), but he has a girlfriend named Steffie (Nicki Minaj). Manny catches Peaches going to the waterfall to hang out with her mammoth friends, along with her best friend, a Molehog named Louis (Josh Gad). Manny had specifically told her not to, and embarrasses her, in front of everyone. As a result, Manny and Peaches argue and have a fall out. Soon after, the separation of the continent separates Manny from his family.

Manny gets stuck on a floating ice "ship" with Sid and Diego (Denis Leary). At the same time, a giant land shift encroaches on those remaining on land. The large moving landmass drives Ellie, Peaches, and a herd of other animals towards a land bridge, where Manny had told them to go before being separated. The land bridge is the link to the other large drifting landmass.

Scrat, lost at the sea, comes across an island and finds a skeleton of a saber-toothed squirrel. The skeleton points towards an acorn-shaped map at the bottom of the ocean, which leads to a mysterious acorn-filled island "The Lost City of Scratlantis". Scrat decides to follow the map and find the island.

After Manny and his friends survive a rough sea storm, they also find Granny, who was inside a tree trunk on the same floating ice shift. Granny had slept through the entire storm and goes for a bath in the ocean, saying that it is her first bath in decades. Sid has to jump in after her to bring her back. Granny calls out for her pet named Precious, which Diego believes is her imaginary friend.

Manny and his friends are captured a group of pirates, led by a Gigantopithecus named Captain Gutt (Peter Dinklage) along with his first mate, a female saber-toothed cat named Shira (Jennifer Lopez). Gutt and the pirate gang attempt to shanghai Manny and his friends, telling him to join the pirates, but he refuses. The pirate crew includes Flynn (Nick Frost) an elephant seal, Squint (Aziz Ansari) a Palaeolagus, Gupta (Kunal Nayyar) a Bengali Badger, Raz (Rebel Wilson) a Procoptodon among others. Most of crew was rescued by Gutt from the sea, just like he rescued Manny and his friends.

Gutt then attempts to make the herd walk the plank, but they manage to escape, in the process destroying the pirate ship when Manny crashes the main mast of Gutt's ship. The ship splits into 2 parts and Manny and his friends are stranded on one part. They rescue Shira, who had been left behind by the pirates.

Gutt promises revenge on Manny by striking his family, as Manny caused the loss of his ship as well as his fruit bounty which is now impossible to replenish. Shira reveals that the way back to the mainland is by catching a current at the Switchback Cove, which runs from an island in the middle of the ocean. The herd reaches the island when their ice drifts towards it and encounters a group of Hyraxes, as well as the pirates, who force captive Hyraxes to build a new ice ship elsewhere on the same island. The herd plans to steal the ship and use it to get home.

Just before they manage to escape aboard the ship, Diego, having fallen in love with Shira, tries to convince her to leave the pirates and join the herd for a better life, but Shira, starting to reciprocate Diego's feelings, while initially accepting, instead stays behind and slows Gutt down so the herd can escape. The herd free the captive Hyraxes and overtake the new ice ship and sail away. Gutt, in anger, quickly creates a new ship, propelled by narwhals, and chases the herd, determined to get revenge on Manny.

Meanwhile, Manny, Sid, Granny and Diego on their way home, encounter sirens, depicted as sharp-toothed creatures who take the shape of loved ones. Fortunately, Manny realizes this and manages to steer the ship away from the sirens.

Later, Scrat meets a siren, which uses the shape of Scratte (Karen Disher), an old flame of his. But Scrat turns away and ignores it. Then, the siren takes the shape of an acorn, causing Scrat to hug it and bury it ("killing" the siren). Scrat is then attacked by the other sirens but is able to get away.

Meanwhile, during the animals' trek to the land bridge back on the mainland, Peaches joins the group of mammoths from before, only to find out that they do not care about the ongoing danger, and they look down on her for being friends with a mole hog named Louis. When Louis overhears Peaches telling the other mammoths that they are not friends, Peaches realizes who her true friends are and berates the others for their cocky attitudes.

Ellie, Peaches, Louis, and the herd of other animals reach the land bridge but find it to be destroyed. Manny, and the gang finally reach home, but much to their horror, find out that Gutt and his pirates had beaten them to it and captured Ellie, Peaches and the herd of animals. Manny attempts to turn himself in to Gutt in exchange for releasing his family, but Gutt prepares to kill his family. Louis comes to their rescue, starting a battle.

Sid and Granny are saved by Granny's presumed "imaginary" pet Precious, a gigantic whale, and defeat the pirates. Gutt engages Manny in a fight atop an ice raft. Manny manages to defeat him by finally smacking Gutt far away with a log. Peaches saves Ellie, while Manny defeats Gutt in a final duel on an ice floe before he is saved by Precious from falling into the ocean.

Gutt encounters a siren that assumes the shape of a female Gigantopithecus, who eats him alive by trapping him in a giant clam. In the aftermath, Peaches reconciles with both Louis and Manny, who is finally reunited with his family and friends, while Shira joins the herd and starts a romance with Diego. With their home destroyed by the land shift, Precious takes the herd to a lush island, where the Hyraxes have started rebuilding their civilization.

Scrat reaches Scratlantis, where there are acorns everywhere, causing him to become eagerly hyperactive. When he is warned not to take anymore, Scrat unsuccessfully attempts resistance but then pulls a giant acorn plug where water comes in and flushes the entire city down, taking its residents with it in the process. Scrat survives, but when trying to dig where the city is now, the ground cracks as Scrat is now in the middle of a desert known as the Death Valley, where his eyes start burning and ends yelling.