The film opens with Peter Rabbit (voice of James Corden) running through the fields where he interacts with all of his woodland friends, including Mr. Jeremy Fisher (voice of Domhnall Gleeson), Pigling Bland (voice of Ewen Leslie), and Mrs. Tiggy-Winkle (voice of Sia), while also evading the hungry Mr. Tod (voice of Fayssal Bazzi). Peter joins his family, cousin Benjamin Bunny (voice of Colin Moody) and Peter's triplet sisters - Flopsy (voice of Margot Robbie), Mopsy (voice of Elizabeth Debicki), and Cotton-Tail (voice of Daisy Ridley) - as they prepare to head into the garden of Mr. McGregor (Sam Neill). The rabbits enter the garden and steal some of McGregor's vegetables before the man spots the rabbits and tries to handle them violently. They are saved by McGregor's neighbor Bea (Rose Byrne), an animal lover and painter. She brings the rabbits into her home where she gives them water with blackberries. Flopsy (being the narrator) mentions that Bea's paintings aren't great, but the drawings she made of the rabbits are actually well done (and in the style of the original books). However, they bring up painful memories, as the drawings reveal that Peter and his sisters lived with their parents until their father went into McGregor's yard and was killed before being made into a pie. Bea looks after the rabbits since their mother is gone too. Peter runs back to McGregor's yard because he left his jacket there, which belonged to his father. He gets it and starts to leave, but McGregor traps Peter and prepares to finish him until nature finishes McGregor first with a heart attack. After his body is taken away in an ambulance, Peter is ecstatic and invites all the animals to McGregor's house since it is now vacant and they can eat and do whatever they want. In London, McGregor's great-nephew Thomas (Domhnall Gleeson) works at a toy store where he makes sure everything is in tip-top shape and is eagerly awaiting a promotion. He is called in to speak to the store's general manager, who informs him that Mr. McGregor died and his house goes to Thomas, who didn't even know he had a great-uncle. After learning that his sought after promotion has been passed onto another employee, Thomas loses it and starts to wreck the store in a fit of rage before he is fired. However, he later learns that the house can be refurbished and put on the market, so he plans to sell it and build his own toy store to rival the one he previously worked at. He takes a cab to the countryside to find the house. The animals have a party in the McGregor house and make a huge mess before Thomas arrives. Everyone runs and hides, just as Thomas enters and sees the mess. He sits down on the couch and finds Pigling, causing them both to scream and forcing the animals to run out of the house. In the morning, Thomas starts to clean up the house. He then starts to close off any opening into the garden, much to Peter's dismay. Bea walks over to introduce herself and insists to Thomas that he leave the gate open for the rabbits to roam freely. She also gives him a pair of binoculars for bird-watching as a gift. Thomas agrees with her on the gate until she walks away and seals it off completely. Peter recruits Benjamin to join him as they find a way into the garden. Thomas spots them and attempts to catch them. He ends up grabbing Benjamin and stuffs him into a bag. Thomas goes to dispose of him, so Peter and his sisters sneak onto his truck to rescue Benjamin. They succeed and put the binoculars in the bag. Thomas accidentally drops them into the river, forcing him to jump in and retrieve them. Thomas drives into town to find supplies to handle his pest problem. He grabs what he needs and almost hits a snobbish couple on his way out of the hardware store, before running into Bea. He gives her a lift home while the rabbits attempt to ride back on the truck, only to get thrown out when it starts moving too fast. They manage to hop back on, and Peter notices with jealousy that Bea appears to be growing fond of Thomas. Thomas and Bea spend more time together, which upsets Peter because he always saw Bea as a mother figure. Peter enters Bea's painting room while Thomas is there, leading her to think that Peter and Thomas are getting along. When she's gone, the two start fighting until Peter accidentally uses a brush to paint over one of Bea's paintings. She gets upset and makes Peter stay outside. The animals start to get back at Thomas by setting up rabbit traps in his bed as well as planting rakes and hoes for him to step on so that he hurts himself. In turn, Thomas sets up traps around the yard, including an electric fence he smears with peanut butter in case they are tempted. Mrs. Tiggy-Winkle goes for the peanut butter, causing her to get electrocuted (non-fatally) and shoot quills at the other animals. Peter and his sisters retaliate and rewire the electricity so that it shocks Thomas until he passes out in the garden. When Thomas gets up, he sets up dynamite in the rabbits' burrow to get them out. Later on, the rabbits attack Thomas in the garden by pelting him with vegetables until Flopsy gets him in the throat with a blackberry. Luckily, he had an epipen on him. Thomas then grabs several sticks of dynamite and lights them before throwing them at the rabbits. Bea can't hear because she's playing music and painting. Moments later, she steps out because she thinks she hears something. The detonator falls out of Thomas's pocket, and Peter picks it up to prove he was using explosives after he denies it to Bea. Unfortunately, they forgot about all the dynamite in the burrow, which causes the tree on top of it to fall on top of Bea's painting room. She is angry at Thomas for what he's done. Thomas sadly goes back into London and manages to get his job back after putting his house on the market. However, Peter feels terrible for what happened since Bea is upset. When he finds out she plans to leave, Peter and Benjamin head into town with a street mouse they meet and eventually locate Thomas at the toy store. He sees the rabbits and chases them into an employee closet. Peter then starts speaking to Thomas and apologizes for what he did and asks for his help in getting Bea to stay. Thomas decides to form a truce with Peter and he leaves the store for good. After a long journey back to the countryside, Thomas stops Bea just before she leaves in a cab. Thomas apologizes for what he's done and says that Peter helped him get back. Bea doesn't believe him until Peter takes out the detonator from his jacket and hands it to Bea. She forgives him, but Thomas is unable to return home because a couple has bought the house - the same snobby couple he encountered in town at the hardware store. Peter and his friends do what they do best and spring their traps to send the couple running away. In the end, Thomas and Bea get together and head back to London with the rabbits where Bea makes illustrations for children's books, including a few stories on Peter and his friends.
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