In the opening scene, a comical and determined Scrat, the saber-toothed squirrel, climbs a glacier, hilariously spewing water after creating a gaping hole in the ice. As the icy world of the Ice Age gradually melts, the local creatures remain blissfully unaware, frolicking in the pools formed by the thawing ice. Among these creatures are our cherished protagonists from the first film: Manfred, Sid, and Diego. In the midst of their fun, Sid decides to set up a day camp for the young animals, but neither the children nor his playful friends take him seriously, leading to some well-deserved ribbing. Feeling disheartened, Sid embarks on a quest to prove his worth.
Sid’s antics lead him on a daring mission, causing Manfred to recount a story to the little ones. But when a curious young songbird inquires about his “big, happy family,” he is rendered speechless, as old memories resurface. Meanwhile, two frightened boys flee from Fast Tony, a sharp-tongued six-banded armadillo and the valley's local con artist, who makes a dire prediction about an impending flood, urging everyone to stock up on bark and reeds that he just so happens to sell. Though Manfred dismisses the alarming claim, his attention is diverted when he sees Sid preparing to dive off a towering waterfall. Rushing to save him alongside Diego, they witness the catastrophic melting conditions of their valley; the inner layers of the massive glacier are thawing, held back only by a fragile outer shell.
Manfred tries to sound the alarm about the impending disaster, yet the other animals laugh off his warnings. A know-it-all aardvark questions why they should heed advice from a species on the brink of extinction. However, the animals' laughter soon dissipates upon the arrival of an intimidating vulture, who suggests that they seek refuge in a giant boat awaiting them at the valley's end. With hair-raising urgency, he mentions the estimated time before the dam breaks: "BOOM!" With that revelation, the animals hurriedly make their way to the boat—only to be followed by Scrat, who inadvertently drives the plot further with his antics. As the chaos unfolds, a glacier containing prehistoric sea reptiles, Cretaceous and Maelstrom, breaks free, sealing their fate as the creatures emerge into this melting ecosystem.
As the journey progresses, Sid pokes fun at Manfred, bringing attention once more to his status as the last mammoth, which is not meant to hurt him but just highlights Sid's naivete. During a solitary stroll, Manfred unexpectedly meets Ellie, his long-lost counterpart, only to realize that she believes herself to be an opossum, along with her mischievous brothers, Crash and Eddie. Sid invites Ellie and her siblings to join their escapade, forcing Manfred to constantly try and convince her of her true identity. Just as he is about to admit defeat, a treacherous encounter with Cretaceous and Maelstrom occurs. Alone, Sid discovers that Diego harbors a frightful secret—he is terrified of water, a truth he struggles to confront.
One evening, as the group takes refuge by a grove, Ellie begins to remember significant moments from her past, leading to the revelation that she is indeed a mammoth. Despite developing a faint romantic tension with Manfred, she recoils when he suggests they work together to ensure their species' survival. However, after a courageous rescue of the herd from a collapsing chasm—quickly directed by Diego—the chemistry between Manfred and Ellie can no longer be denied.
Meanwhile, a hilarious twist of fate leads to Sid being captured by a tribe of mini-sloths, who mistakenly idolize him as a god. Believing he has finally gained the respect he craved, things take a comical downturn as the tribe plans to sacrifice him to avert the flood. Sid manages to escape and unsuccessfully tries to convince his friends of his wild encounter. The group soon encounters the vultures in a Broadway-style performance titled "Food Glorious Food," which underscores the dangers they face. They finally arrive at the gigantic boat, only to confront a field of hot geysers obstructing their path. An argument ensues between Ellie and Manfred regarding which route to take, resulting in the group splitting into two.
In a tense moment, Manfred makes it past the geysers and reaches the boat, but he frantically searches for Ellie, only to be met with devastating news from Crash and Eddie about her fate. A mountainside collapses, trapping Ellie in a cave while others struggle to escape the rising floodwaters. As Manfred dives in to save her, Diego confronts his fear of water and rescues Sid alongside their comrade Crash and Eddie. A climactic battle unfolds with Cretaceous and Maelstrom, leading to a tense showdown where they are ultimately vanquished.
Manfred succeeds in rescuing Ellie and finally shares a romantic moment, but their reprieve is short-lived as the floodwaters continue to rise. As the animals on the boat witness the calamity unfold, Scrat makes a desperate climb and, through a series of mishaps, unintentionally alters the course of the flood and saves the valley's creatures. However, believing he has perished, his friends mourn him.
In an uplifting turn of events, a herd of mammoths emerges from beyond the glacier rift, eliciting expressions of disbelief and joy from the animals, especially Ellie and Manfred. Yet soon, Manfred grapples with conflicting emotions, recognizing the absence of an excuse to be with Ellie for the sake of their species. She hints at her desire to be with him, but after a misunderstanding, she departs with the herd. However, Manfred chases after her, inspired by Diego and Sid. He confesses his true feelings, culminating in a heartwarming reunion where the herd rejoices in their newfound bond, leaving the duo stronger than ever. Sid and Diego, initially forlorn, are pleasantly surprised by the fact that the herd, including Manfred and Ellie, has committed to remaining together, highlighting the enduring friendships and love that define their world.
