Plot
After the events of the previous film, Paddington Bear is given a passport and an umbrella by his neighbours at 32 Windsor Gardens.
Despite living in the same house, the Brown family has drifted apart. Judy is applying for admission to a university in the Faroe Islands, and Jonathan spends most of his free time relaxing in his room. Mrs. Brown has started working on a new art project, while Mrs. Bird tackles her long to-do list and Mr. Brown deals with his new boss from the United States who encourages him to take more risks.
Paddington receives a letter from the Home for Retired Bears in Peru, informing him that his aunt Lucy is acting strangely and deeply misses him, so Paddington and the Browns decide to travel to Peru to visit her. Upon their arrival, the Browns learn from the Reverend Mother that Lucy has gone missing in the Amazon rainforest, leaving behind only her glasses and her bracelet. Paddington finds a map in Lucy's cabin highlighting a location named Rumi Rock and decides to travel there to start his search, taking Lucy's bracelet with him. Mrs. Bird stays behind with the Reverend Mother, who gifts Mrs. Brown a pendant for good luck.
Looking to hire a boat to travel down the river, the Browns meet riverboat captain Hunter Cabot and his daughter Gina. Hunter notices Paddington's bracelet and informs the family of El Dorado, a mythical city said to contain the gold offered by ancient Peruvians to the jungle spirits. Hunter warns Paddington that travelers in search of El Dorado typically begin their searches at Rumi Rock, but do not return alive. It is later revealed that Hunter is driven by the ghosts of his ancestors to find gold at any cost, and plans to hijack the trip to find El Dorado himself; he argues with Gina about continuing the journey, with Gina wanting him to turn back. Hunter responds by throwing Gina off the boat, but then falls overboard himself, causing the boat to shipwreck.
In the ensuing confusion, Paddington is separated from the Browns and stumbles upon Rumi Rock, where he finds Hunter waiting for him. After hearing roars that Paddington believes are calls and responses from himself and Lucy, Hunter sets off with Paddington in search of Lucy and El Dorado. Meanwhile, Gina finds the Browns and explains her father's motivations and family history; they set out to find Paddington and save him from Hunter. Mrs. Bird grows suspicious of the Reverend Mother and follows her into a secret room, where she reveals that the pendant she gave to Mrs. Brown is actually a tracker. Now knowing their location, Mrs Bird and the Reverend Mother fly a plane into the forest to rescue the Browns.
Hunter and Paddington reach the summit of an Incan fort, which contains a slot that matches the emblem on Paddington's bracelet. Hoping to take the bracelet for himself, Hunter attacks and chases Paddington, but the Browns arrive just in time to save him. The Reverend Mother arrives and reveals herself to be Clarissa Cabot, Hunter's long-lost cousin who faked her death and also wishes to find El Dorado. Clarissa further reveals that she staged Lucy's disappearance to lure Paddington to Peru, and holds the Browns and Gina at gunpoint. Hunter intervenes and incapacitates Clarissa, ridding himself of the visions of his ancestors. The Browns use Paddington's bracelet to enter El Dorado, where they find Lucy, who explains that El Dorado is an orangery where Paddington was born. She says that her bracelet originally belonged to Paddington and the bears of El Dorado. Paddington bonds with the other bears making marmalade, but ultimately chooses to return to London with the Browns.
Afterwards, Hunter reconciles with Gina and gives up his obsession with gold. Clarissa is sent to the North Pole to become a real nun and work at the Home for Retired Polar Bears, much to her dismay. Several bears from El Dorado visit Paddington in London, and are named after other London rail stations. Paddington and the bears visit convicted actor Phoenix Buchanan in prison. Believing that he will soon be released, Buchanan plans a production of "Goldilocks and the Three Bears" starring the El Dorado bears.
