While raiding Berk's Squab Farm, Mr. Fox inadvertently triggers a fox trap, capturing himself along with his wife, Felicity. It is during this tense moment that she reveals her pregnancy, imploring him to pursue a safer career if they manage to escape. Mr. Fox agrees, promising to change his ways.
Fast forward two years (12 fox-years later), the Fox family, including their son Ash, is adjusting to life in a cozy hole. Now a newspaper columnist, Mr. Fox decides to upgrade their living situation to a magnificent home inside a tree. Ignoring the cautionary advice from his lawyer, Clive Badger, Mr. Fox is oblivious to the dangers posed by the nearby farms of three menacing farmers: Walt Boggis, Nate Bunce, and Frank Bean.
Shortly after their move, Felicity’s cousin, Kristofferson Silverfox, comes to stay with them while his father undergoes treatment for double pneumonia. While the Foxes embrace him, Ash struggles with jealousy, feeling overshadowed by his charming cousin who seems to excel at everything. Nostalgic for his days as a thief, Mr. Fox, along with his opossum friend, Kylie, the superintendent, plans a series of daring raids to steal food from the farmers' lands. The tension escalates as the outings stir Ash's resentment further, especially when Mr. Fox conceals them from Felicity, who becomes increasingly suspicious when mysterious supplies appear in their pantry.
Furious over the thefts, the farmers conspire to eliminate Mr. Fox. They lay in wait near his residence, and when Mr. Fox finally appears, they open fire, only managing to shoot off his tail. Their attempts to unearth him are thwarted when they find out the Foxes have cleverly dug an escape tunnel. Recognizing their need to surface for food and water, the farmers prepare for a showdown at the tunnel entrance. Meanwhile, beneath the ground, Felicity is distressed by her husband's return to his old thieving ways.
As their plight deepens, they encounter Badger and other local animal residents who have also lost their homes to the farmers' ruinous actions. Faced with the specter of hunger, Mr. Fox rallies the group, organizing a radical digging operation to access the farmers' properties and raid their stock. During these escapades, Ash and Kristofferson begin to mend their frosty relationship, especially when Kristofferson heroically defends Ash from a bully.
However, the farmers retaliate by flooding the animal tunnels with Bean’s cider, forcing the creatures to retreat into the sewers. In a moment of determination, Ash and Kristofferson sneak back to Bean's farm to recover Mr. Fox's missing tail. Unfortunately, Kristofferson is captured, and it soon becomes apparent that the farmers intend to use him as bait to trap Mr. Fox. In a moment of bravery, Mr. Fox decides to confront them but is met with aggression when Rat, Bean’s brutish security guard, attacks. A fierce confrontation ensues, culminating in Rat being fatally electrocuted. Before he meets his end, he divulges that Kristofferson is imprisoned in the attic of Bean's Annex, igniting a daring rescue operation spearheaded by Mr. Fox.
Mr. Fox arranges a meeting with the farmers in Paddington, offering to surrender if they release Kristofferson and spare the rest of the animals. However, the farmers set a trap, only for the animals to counteract it with their own cunning plan, allowing Mr. Fox, Ash, and Kylie to infiltrate Bean's Annex undetected. Ash proves his mettle when he braves the chaos to unleash a rabid beagle on the farmers, effectively securing their escape with Kristofferson in tow.
As the farmers anxiously await the animals' emergence from the manhole, Mr. Fox and his family settle into their new sewer homes, inviting other animals to join them. Finally, in a celebratory mood, Mr. Fox leads a raid on a supermarket owned by the farmers, where Felicity joyfully announces her pregnancy once more. The scene culminates with a jubilant dance among the animals, marking the arrival of a bountiful new food source.
