In the next shot, the creatures of the Ice Age are all shown enjoying themselves on slides and pools made by the melting ice; among them the three protagonists of the first film: Manfred, Sid, and Diego. Sid opens a day camp, where none of the younger creatures take him seriously, nor do Manfred and Diego, which leaves Sid seeking a daring deed for more respect. Soon, the trio discover Fast Tony and Stu, a pair of local con artists claiming that the earth will flood and that the bark and reeds which they sell are needed to snorkel and stay aloft. Manfred dismisses the idea, but is distracted when he sees that Sid will try to high dive from a giant waterfall; as Manfred goes with Diego to the top of the waterfall to save Sid from his act of daredevilry, they see that the global warming caused the ice of the valley to melt, and it is kept from destroying the valley only by the glaciers, which have formed a dam. It is then that a turkey vulture known as the Lone Gunslinger tells the animals that a giant piece of a fallen tree can act as a boat and save them from the floods; all soon set out to find it.
During the time that the masses of animals escape, a glacier which contains two sea reptiles from the Mesozoic era, (Cretaceous and Maelstrom), breaks off. The con-man Stu is an example of these reptiles' hunger as he is soon devoured, leaving behind his shell alone.
Along the way, Manfred grows unhappy when other animals tease him about being the last mammoth alive. Manfred takes his leave for a moment, leaving Diego and Sid alone, unknowingly to be heckled by two opossums named Crash and Eddie. The opossums proceed to torture Sid and Diego, shooting pebbles at them and baiting them to fight in the manner of Whac-A-Mole. Meanwhile, Manfred meets Ellie, a female mammoth who believes she is an opossum and the sister of Crash and Eddie. Sid invites her to tag along with the group to escape the flood, and she brings her brothers, who spare no chance at their pranks.
After a perilous ordeal with Cretaceous and Maelstrom, Sid finds out that Diego is afraid of water. As they walk Ellie plays with her brothers and gets stuck under a log. Manfred lifts it off her and it opens up an area which Ellie recalls from her childhood as the place where she was adopted by her brothers' mother. She finally realises she is a mammoth and starts getting along with Manfred but grows apart from him when he suggests "saving their species". In time, when the situation calls for it, to save them all from falling into a gorge of pointed rocks, they make up. During the night, while all are asleep, Sid is kidnapped by a tribe of mini-sloths (small multi-coloured sloths) who believe Sid to be a god. Sid lights a fire for them, and believes that he has found respect as their deity, but they plan instead to sacrifice him to a volcano. Sid escapes this fate and returns with his herd.
The next morning, Manfred and the others regroup with Sid, who regales them with his experience with none convinced, and they all find out that they had overslept. As they all rush to reach salvation, they find a field of hot geysers, which separate Manfred, Sid, and Diego from Ellie and her brothers. Each group believes in espacing the geysers differently(Namely Manny and Ellie).
When the flood comes, Manfred saves Ellie from drowning as she is caught in a grotto of rocks, while Diego overcomes his fear of water to save Sid. All is about to be ruined when Cretaceous and Maelstrom come about, but due to Manfred's quick thinking, they are finished off by a rock which falls on them. While all this happens, the other animals are taken on a death ride on the "boat" as it floats about, and are off at the mercy of the water currents.