In an attempt to bury his acorn, Scrat inadvertently causes the break up of Pangaea. Meanwhile Manny and Ellie must deal with the trials and tribulations of their daughter Peaches, now a teenager desiring to fit in with her peers. Her only friend is Louis, a molehog who, out of an apparent crush, tries to protect her as she tries to approach a mammoth named Ethan whom she has a crush on. Sid's family returns, only long enough to dr
op off the elderly Granny before abandoning them both again. The continental division then breaks apart a family argument between Manny and Peaches, who had snuck off to meet Ethan. Trapped on a moving chunk of ice with Sid and Diego, Manny has no choice but to ride out the current, separating him from his family. Meanwhile a giant land shift encroaches on Ellie, Peaches, and those remaining on land, causing them make their way toward the land bridge.
At sea, violent weather pushes Manny and the others further away from land while Scrat, in a side adventure, finds an acorn that has a treasure map on it that directs him towards an island. Soon, after Manny, Sid, and Diego find Granny (who was sleeping inside a hollow tree stump, on the ice raft), they are captured by a band of pirates sailing on a floating iceberg as a ship led by a Gigantopithecus, Captain Gutt, who attempts to press gang them into his crew; when they refuse Gutt tries to make them walk the plank. Manny, Sid, Diego, Granny and Scrat (who was also taken captive) escape, but cause the ship to sink and Gutt's first mate, a female sabertooth named Shira joins them out of no choice of her own.
They then find Switchback Cove, which has a current that would direct them home, after washing ashore a remote island, but Shira escapes and tells Gutt and the pirate crew (who are also on the island) of their whereabouts. Gutt, wanting revenge on Manny for sinking his ship, plans an attack. Along with the hyrax inhabitants of the island, Manny coordinates a plan to steal Gutt's new ship to return home. Shira decides to leave Gutt, when she and Diego begin to fall in love, but she stays behind to ensure Gutt doesn't catch the herd. Gutt and his pirates quickly make a new iceberg ship to sail after the herd, determined to get revenge. Meanwhile, Scrat, using one of the hyrax's leaf "planes," flies off the island, only to be swallowed by a shark.
Peaches finally begins to fit in with the mammoths her age, but accidentally insults Louis, who is referred to as a freak by the others, by saying they are not friends. When she sees the other teens' careless disregard to the danger, she turns her back on them, warning that their extinction will come sooner than they think.As they are sailing back, Diego, Sid and Granny encounter monstrous sirens taking the shapes of what the group finds most attractive. Fortunately, Manny realizes this after hearing a siren, disguised as Ellie tell him something she would never say and saves them at the last second. Later, Scrat encounters a siren, taking on the shapes of Scratte (that Scrat ignores) then an acorn. Scrat immediately runs up and attempts to bury the "acorn", but is attacked by other sirens and escapes unharmed.Manny, Sid, Diego, and Granny soon return home only to find the land bridge destroyed in the earthquakes and Gutt and the pirates are there, holding his family hostage. Louis stands up for Peaches and a battle ensues between the herd and the pirates. Shira frees Ellie and helps fend off her former comrades, while Granny's previously unseen (and claimed imaginary) pet whale Precious appears and turns the tables on the rest of the lot. Gutt then attempts to kill Ellie, but Peaches, using her possum-like skills, manages to save her. Manny defeats Gutt in a duel and reunites with his family and friends. Later, Gutt encounters a siren taking on the shape of a female of his species and is eaten. The entire party and inhabitants then sail to an island that they found to settle down. Manny allows Peaches to "have an adventure" having gained a new respect for her and toward Louis. Shira joins the herd and becomes Diego's lover, while Louis becomes a hero among the teenage mammoths.At the end of his journey, Scrat discovers the island on the map, know as Scratlantis (a mock up of Atlantis), but his uncontrollable urge to hunt acorns in the acorn-rich city inadvertently causes the entire island to sink and Scrat is ejected into what is now known as Death Valley'Ray '