When Blu, a domesticated macaw from small-town Minnesota, meets the fiercely independent Jewel, he takes off on an adventure to Rio de Janeiro with the bird of his dreams.

Times are changing for Manny the moody mammoth, Sid the motor mouthed sloth and Diego the crafty saber-toothed tiger. Life heats up for our heroes when they meet some new and none-too-friendly neighbors – the mighty dinosaurs.

Manny, Sid, and Diego are currently living in a large valley surrounded by an enormously high ice wall on all sides. However, the trio discovers that the ice wall is actually a dam that is barely holding a massive body of water that could flood the valley to nearly a mile underwater. A vulture tells them that there is a boat at the other end of the valley that may save them all, but they only have three days to reach it or die. Manny is also having trouble fearing the fact that he may be the last mammoth left.

Spix's Macaws Blu and Jewel and their three children—Bia, Carla, and Tiago—are living happily Rio de Janeiro until Jewel realizes that her children are becoming more like humans. Meanwhile, Blu's former owner, Linda Gunderson and her Ornithology husband, Tulio are on an expedition in the Amazon rainforest and, after a fall down a waterfall, discover a quick-flying Spix's macaw that loses one of its feathers. When word gets out about this through television, Jewel believes that they should go to the Amazon to help find the blue macaws. While the kids are ecstatic, Blu is uncertain, but he is pressured into going along. Rafael, Nico and Pedro decide to come along. Luiz attempts to follow but fails. Blu brings a fanny pack full of supplies, one of which he uses mostly is a Global Positioning System, much to Jewel's displeasure.