Manny becomes over-protective about his teenage daughter Peaches going to the falls to see a teenage mammoth called Ethan. Manny's wife Ellie calms him down and tells him that Peaches is not going to be his little girl forever. Peaches, along with her best friend, a molehog named Louis, go to the falls, but Manny stops them and takes Peaches home. Meanwhile, Sid reunites with his family, but is abandoned again, with his obnoxious Granny that wanders away, The Herd looks for her. Manny catches Peaches with Louis heading to the falls; he finds her with Ethan and Manny embarrasses Peaches in front of her friends Upset at Manny, Peaches said that she wish Manny was never her father. Soon after, the separation of the continents separates Manny from his family. Manny gets stuck on a floating iceberg with Sid and Diego. A large moving landmass drives Ellie, Peaches, and a herd of other animals towards a land bridge, where Manny had told them to go.
After Manny and his friends survive a rough sea storm, they also find Granny, who was inside a tree trunk on the same floating iceberg the entire time. Manny and his friends are captured by a group of pirates, led by a Gigantopithecus named Captain Gutt along with his first mate, a female saber-toothed cat named Shira. Gutt and the pirate gang attempts to get Manny and his friends to join their crew (by singing them a song to introduce Gutt along the way), but they refuse. Gutt then attempts to make them walk the plank, but they manage to escape, destroying the pirate ship in the process. Gutt and the pirates are separated from Shira, and the pirate crew worries about her, but Gutt leaves her for dead. Meanwhile, Shira gets rescued by the herd.
The herd reaches an island and when they arrive Shira escapes, but Diego finally captures her. The herd found a way home and 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. They find some free hyraxes and ask them to help them steal the ship (thanks to Sid's communication), that night they set up plan to steal the ship and free the captive hyraxes. The next morning, the herd and the hyraxes' plot to steal the ship and free the captive hyraxes was prepared.
Shira later escapes and rejoins the pirates, but finds herself being berated and called a failure by Gutt for not trying to kill the herd and as punishment, he relieves her of her position while giving it to Squint. The herd puts the plan into action and successfully takes the ship and frees the hyraxes. Shira captures Diego, he tells her she should join Manny and the herd, and leave the pirates. She lets him go and buys them have some more time to escape and help them prevented Gutt from catching them. After the herd and the hyraxes leave freely, Gutt, quickly creates a new ship, by breaking off a chunk of ice from a nearby ice wall and calls out for his narwhals to propel it. He threatened Shira to be killed and so the pirate gang sets out after the herd, determined to get revenge on Manny.
Back at the continent, Peaches visits an underground hideout with Ethan and his group. To be accepted, she says she is not friends with Louis. Louis overhears her, and he leaves heartbroken. Meanwhile Manny, Sid, Granny and Diego, are on their way home, Diego worried about Shira, and Manny and Sid figure out that Diego is in love. Soon enough, they encounter sirens, depicted as sharp-toothed creatures who take the shape of loved ones Diego sees Shira, Sid sees an attractive female sloth, Granny sees a hunky surfer sloth ,forming a facial hair, and Manny sees Ellie and Peaches. Fortunately, Manny realizes this and manages to steer the ship away from the sirens.
Ellie, Peaches, Louis, Crash, Eddie, and the herd of other animals reach the land bridge, but find it to be destroyed. Manny, and the gang finally reach home, and also find the land bridge destroyed, but Manny happily finds Peaches. Much to their horror, Gutt and his pirates have beaten them to the bridge, and captured Ellie & Peaches. Manny attempts to turn himself in to Gutt in exchange for the release of his family, but Gutt prepares to kill Ellie and Peaches, as he still wants revenge on Manny. Louis comes to their rescue. Gutt teased Lewis and tosses him a sword (smiler to the one from third film to fight him, but Lewis is able to defeat him and free Peaches with his own skills. The Battle stars, Sid and Granny are saved by Granny's presumed "imaginary" pet, Precious, a gigantic whale, and they defeat the pirate crew. Peaches defeats Gutt by using her half-opossum skills and saves Ellie, causing Manny to realize that he had been wrong about Peaches. Gutt recovers and engages Manny in a fight, a landmass suddenly burst out of the ocean, causing a chunk of the ship where Manny and Gutt were on to break and slide down the landmass. Manny manages to defeat him by moving to the edge of the iceberg, causing Gutt to soar upward, and finally, Manny smacks Gutt far away with a log. The iceberg slips off the landmass, causing Manny to fall off the iceberg. He is about to land into the ocean, but gets rescued by Precious, Sid and Granny. Meanwhile, Gutt recovers, but finds a siren disguised as a female Gigantopithecus, Gutt goes up to it and gets killed.
Manny reunites with his family and reconciles with Peaches, Shira becomes Diego's girlfriend and joins the herd, Manny and Diego tells Sid and Granny that there not screw-ups but a heros. Louis also becomes a hero among the other Mammoths, and let him hang out with them. With the continent being destroyed by the landmass the herd and the other animals then find another continent (where the hyraxes have also gone) which they accept as their new home with new beginnings.
Scrat's 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 and chasing his acorn around it. This causes the land on the earth's crust to break and separate into seven continents, Scrat finally catches his an acorn and gets shot out of the earth's inner core and lands on a small iceberg that breaks in two that separates Scrat from his acorn.
Scrat, lost at the sea, comes across an island and finds a skeleton of a sabre-toothed squirrel. The skeleton points towards an acorn-shaped map at the bottom of the ocean, which leads to a mysterious acorn-filled island. Scrat decides to follow the map and find the island. As he begins his journey, he is captured by the group of pirates that capture Manny, Sid, Diego, & Granny but manages to escape when the ship breaks in two.
Later, after the pirates gone after the herd for revenge, Scrat sets off for his journey by trying to fly on one of the leaf-gliders, but he gets pushed on an ice wall by the wind, but finally flies away.
Later, after the herd escaped the sirens Scrat meets a siren, which uses the shape of Scratte, an old flame of his from the third film, but Scrat turns away and ignores it. Then, the siren takes the shape of an acorn, causing Scrat to hug it and attempt to bury it (which aggravates the siren). Scrat is then attacked by the other sirens, but is able to get away alive.
Finally the film ends with Scrat completing his journey and reaching the island on the map, Scratlantis (a parody of Atlantis); a floating city filled with other sabre-toothed squirrels and acorns. Scrat, excited and gleeful, grabs many acorns on the island in a frenzy and eventually grabs a giant one used as a plug blocking a hole, which causes the city to flood and sink, leaving Scrat in the middle of a desert in North America.