The story follows Blu (originally voiced by Jesse Eisenberg) and Jewel (originally voiced by Anne Hathaway) as they leave their comfortable domesticated life in Rio de Janeiro to raise their three children in the wild. Along the way, they discover an entire hidden tribe of Spix's macaws—including Jewel's long-lost father, Eduardo.
The film takes place three years after the events of the first movie, where Blu and Jewel have built a nest and are raising their three children, Rio, Luna, and Jewel Jr. However, their peaceful life is disrupted when Jewel becomes restless and decides to leave the nest to explore the Amazon rainforest. Blu and their children follow her, and they soon find themselves on an adventure through the dense jungle.