Manny and Ellie are enjoying their lives with their now teenage daughter, Peaches. While Ellie is supportive of Peaches' wish to explore and make new friends, Manny has taken on a more protective role, which often frustrates Peaches and creates tension between them. In the midst of this family dynamic, Sid faces a unique situation as his family comes back to drop off the elderly Granny, only to abandon both Sid and Granny shortly thereafter. The situation escalates when Manny discovers Peaches spending time with a group of teenage mammoths that he disapproves of, leading to a heated dispute between father and daughter.
Then, everything changes following a sudden continental break-up triggered by Scrat's obsession with burying his acorn traps. This event results in Manny, Sid, Diego, and Granny becoming trapped on floating ice chunks, forcing them to drift away from the mainland and leaving Ellie, Peaches, and the rest of their animal friends behind. Knowing their argument weighs heavily on her mind, Peaches feels guilty about their recent conflict. Meanwhile, those left on land face an impending threat from a large land shift that makes their situation increasingly dire, under Ellie’s leadership, they must find a way to cross to safety via a land bridge.
While this unfolds, Scrat discovers a broken acorn at the bottom of the ocean, which reveals a map to “The Lost City of Scratlantis.” Enticed by the prospect, he begins his quest for this mythical city. However, Manny and his crew are not given a moment's rest as they encounter a violent hurricane that propels them deeper into the ocean, where they find themselves captured by a gang of pirates led by the imposing Captain Gutt, a Gigantopithecus who pressures them to join his crew. When Manny refuses, Gutt threatens their lives, leading to a daring escape that inadvertently causes their pirate ship—and its valuable supplies—to sink. Along the way, Shira, a sabretooth and Gutt's first mate, is rescued by the crew after being abandoned by her comrades.
Eventually, they wash up at Switchback Cove, gaining a current that helps them approach home. Realizing that Captain Gutt has enslaved a group of hyraxes to construct a new ship, Manny devises a plan to liberate their fellow creatures and commandeer the vessel. Just as they prepare to leave with the ship, Diego, who has developed feelings for Shira, tries to persuade her to abandon her life as a pirate for a better one with them. While she initially agrees, Shira ultimately decides to stay behind to help Manny's group escape, thus setting the stage for Gutt's revenge.
Meanwhile, back on the mainland, as Peaches integrates with the same group of teenage mammoths, she soon realizes that they are indifferent to the prevailing threats and even disparage her friendship with Louis, a mole hog. When Louis overhears her doubts about their friendship, Peaches understands her true allies and confronts her so-called friends about their arrogance.
After an intense confrontation with a pack of dangerous sirens—predatory mudskippers that lure their prey with false images—the group faces yet another challenge upon their return home. They discover that Gutt has captured Ellie, Peaches, and the remaining herd. As Louis courageously confronts Gutt to rescue Peaches, Granny's beloved pet whale, Precious, arrives just in time to help fend off Gutt's crew. A final battle ensues where Peaches heroically saves Ellie, and Manny ultimately defeats Gutt in an epic duel atop an ice floe; he is saved from plunging into the ocean by Precious.
In a surprising twist, Gutt meets his end when a siren, disguised as a female Gigantopithecus, consumes him by trapping him inside a gigantic clam. Following this climactic struggle, Peaches reconciles with both Louis and Manny, who is finally reunited with his family. Shira decides to join the herd, embarking on a budding romance with Diego. With the land destroyed by the shifting terrain, Precious carries the animals to a lush island where the hyraxes begin rebuilding their society.
Meanwhile, Scrat reaches Scratlantis, a wondrous place filled with acorns, which sends him into a frenzied state of excitement. However, as he is warned against taking more acorns, he attempts to resist his urges but ultimately pulls a giant acorn plug, causing Scratlantis to flood catastrophically. While he survives the deluge, he finds himself in a desolate desert now known as Death Valley, where his eyes begin to burn as he struggles to dig for the drowned city.
