Blue macaws Blu and Jewel and their three children—Bia, Carla, and Tiago—are living happily in the city until Jewel realizes that her children are becoming more like humans. Meanwhile, Blu’s former owner, Linda Gunderson and her ornithologist husband, Tulio are on an expedition in the Amazon 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 GPS, much to Jewel’s displeasure.
Meanwhile, the leader of a group in a line of illegal logging named Big Boss, discovers Linda and Tulio’s expedition to find the macaws and orders his henchmen to hunt them down to avoid disruptions to their work. Also, Blu and Jewel’s old nemesis, Nigel the cockatoo, has survived the plane crash from the first film, but he is now unable to fly and is working as a fortune teller/con artist. When he sees Blu and his family flying overhead, he immediately decides to seek revenge on them. He enlists two minions to help him in his plans; a silent anteater named Charlie and a poison dart frog named Gabi, who is in love with Nigel. Blu and his family use a boat to get to the jungle (with Nigel’s first plan of revenge being inadvertently foiled by Charlie); and, when they arrive, they find nothing. However, they are eventually taken to a flock of blue macaws that are hiding in a secret paradise land. There, they meet Jewel’s stern long-lost father, Eduardo, his older sister Mimi, and Jewel’s childhood friend, Roberto. Eduardo seems unimpressed with Blu’s domesticated human behavior.