Plot
Thomas McGregor and Bea get married, with their friends, human and animal, attending, while Peter Rabbit accepts having Thomas in his life. A month after their honeymoon, Thomas helps Bea as she works on her children's storybook based on Peter and his friends, but Peter is disappointed that the book portrays him as naughty. After getting a letter from a publishing company wanting to distribute the book, Thomas and Bea take Peter, Benjamin, Flopsy, Mopsy, and Cottontail to meet the publisher, Nigel Basil-Jones, who presents his marketing plan which paints Peter as a troublemaker and shows a billboard design for a potential movie that makes him look villainous.
Dismayed, Peter walks away from the group and goes into town where he meets an older rabbit named Barnabas, who claims to be an old friend of his late father. They are snared by animal catchers, who take them to a pet pound, where they were taken in by a girl named Amelia. Barnabas and Peter raid the family's fridge with the help of Barnabas’ crew, and take the food back to their hideout. Barnabas talks about how his father used to steal for Peter and his sisters to keep their bellies full until Thomas and Bea find Peter and bring him home. The next morning, Peter tells Benjamin about Barnabas and convinces him and his sisters to join him in meeting the crew. Recognising Peter's sisters and Benjamin, Barnabas divulges his big plan to rob from the farmers market, with their big score being packs of dried fruit. The rabbits gather help from their animal friends to pull off their heist.
Thomas and Bea meet with Nigel again to go over the designs for the rabbits, but after already having them dressed up in contemporary clothes, Nigel makes more suggestions for the next book. Thomas starts to realise that Nigel's ideas are not in the best interests of Bea's work. The animals arrive at the market and get away with the dried fruits, but all of Peter's friends, including Benjamin and the sisters, are captured by the animal catchers when they sneak into a petting zoo. Barnabas reveals he was intending to keep the dried fruit for himself, while explaining that, after being rejected by humans in the pound due to his old age, he intentionally met Peter in town after reading about him in his book, never even knowing his father.
Feeling guilty, Peter leaves Barnabas and enlists Thomas to help rescue his friends. After hitting a snag with their truck, they go to Bea for help while she is in a meeting with Nigel who wants to put Peter and his friends in a ludicrous space adventure as well as a dangerously unpredictable rescue mission as a way to end the story. Bea pulls her stories from Nigel's company and helps Thomas and Peter rescue their friends while going on over-the-top missions to find them. Peter and his family then go to Barnabas's hideout where they turn the tables by tying Barnabas and his crew to ropes so that they can get pulled away when the nearby tailor shop owner leaves in his truck, leading them to get taken to the pound. The rabbits return the dried fruit to the market sellers, and rejoin Thomas and Bea as they drive home, with Peter deciding to be more willing to listen to the ones that love him. Some time later, Thomas and Bea became parents to a baby girl and Bea names the new book "Peter Rabbit 2: The Runaway”.