After the herd herd survived a rough storm, they find Granny in a tree on the same iceberg. Later the herd encounters an ice ship, and discover that there are a group of animal pirates, led by a Gigantopithecus named Captain Gutt along with his first mate, a female smilodon named Shira. Gutt and the pirate gang attempt to get the herd to join their crew, but they refuse, prompting Gutt to hold them as hostages. Gutt then attempts to make them "walk the plank" with narwhals swimming underneath the edge, but they manage to escape, breaking the pirate ship in the process. Gutt and the pirates survive the incident and is seen floating on their half of the broken ship. Some of the pirates are concerned over Shira's whereabouts, but Gutt leaves her for dead. Meanwhile, Shira, lost at sea, gets rescued by the herd on there half of the broken ship.
The herd reaches an island and they find a way home, and the pirates, leading to forcing some hyraxes to steal Gutt's ship. The next morning, the herd and the hyraxes' plot to steal the ship and free the captive hyraxes is 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, as he relieves her of her position while giving it to Squint as punishment. Diego is captured by Shira, but tells her to join the herd, and so Shira helps the herd to escape and the hyraxes left freely. Gutt who is furious at what had happened, 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. The pirate gang sets out after the herd, as Gutt is now determined to get revenge on Manny.
As the herd head for home, they encounter sharp-toothed sirens who seduce anyone by taking the shape of loved ones. Fortunately, Manny immediately realizes this and manages to steer the ship away from the sirens, before Sid, Diego, and Granny can get any closer to them.
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 also found it destroyed. Much to their horror, Gutt and his pirates have 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, but Peaches defeats Gutt by using her half-opossum skills and saves Ellie. Gutt recovers and engages Manny in a fight when a landmass bursts 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. As he is about to land into the ocean, Manny gets rescued by Granny's "imaginary" pet Precious, with Sid and Granny "commandeering" Precious. 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 and Louis is finally allowed to still be with Peaches whenever she hangs out with Ethan's gang. With the continent being destroyed by the landmass, the herd and the other animals then find another continent which they accept as their new home.
Scrat subplot
When Scrat attempts to bury his acorn at the tip of a mountain, he causes it to break in two. Scrat then falls down into the Earth's inner core and chases his acorn around it, causing the land on the earth's crust to break and separate into seven continents and he gets shot out of the earth's inner core. He lands on a small piece of ice that breaks in two, separating 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 at the bottom of the ocean. Scrat finds a heavy rock and goes down to the bottom of the ocean and discovers the acorn was a map that leads to a mysterious acorn-filled island. Scrat decides to follow the map and find the island.
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.
Scrat completes his journey and reaching the island on the map, Scratlantis; 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 tries to grab a giant one used as a plug blocking a hole, which causes the city to flood and sink, leaving Scrat stranded in the middle of a dry desert in North America.