Blu and company are forced to return to Rio early due to a serious problem. However, while in Rio, they are forced to deal with some old foes, particularly a cockatoo who is out for heated revenge against them and he kidnaps the group's children as bait for the adults. Blu and company must rescue their kids and confront Nigel and his dog friends once and for all.

High King Peter is badly poisoned by a cake and only an exclusive potion made from nine unique ingredients can save him. Worse, a number of youngsters are lured away and end up in a mysterious ocean liner. Kushanku and company must get the ingredients for the potion to save Peter and rescue the kidnapped victims but they also must deal with a new and deadly villain as well.

Aurora, Bellatrix and Sirius and their friends and families follow Blu and company's flight path into the Amazon. However, while Aurora, Orion, Ferdinand and their families adapt well, Sirius and Bellatrix face problems with the EXTREMELY anti-human glaucous macaw clan, such as their stubbornness and views of human-raised animals which they derogatorily call 'mud-pets'