When Tony Stark's world is torn apart by a formidable terrorist called the Mandarin, he starts an odyssey of rebuilding and retribution.

The first scene shows Agent Sam Stanley and Agent Chet Desmond late at night after performing the autopsy on the body of List of Twin Peaks characters#Teresa Banks as they discuss how much time had passed since they entered the morgue. Later, they arrive at Hap’s Diner, where Teresa once worked the night shift as a waitress, and question the owner of Hap’s about Teresa. Sheriff Cable of Deer Meadow goes outside with Desmond, and fights him over taking the body of Teresa with him back to Portland, which took the murder investigation out of the hands of the local and corrupt Police Department. Later, Special Agent Dale Cooper is shown in a doorway in the Philadelphia headquarters of the FBI talking to his secretary Diane. Next, Cooper meets Sam Stanley after Desmond went missing.

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.