As Thomas McGregor (Domhnall Gleeson) and Bea (Rose Byrne) embark on their married life, their circle of friends, both human and animal, comes together to celebrate their love. Initially wary, Peter Rabbit (James Corden) has now embraced the changes brought by Thomas. However, as they bask in the afterglow of their honeymoon, complications arise when Bea dedicates herself to creating a children's storybook featuring Peter and his friends. Peter, disheartened by his portrayal as a mischief-maker, grapples with the implications of this narrative.
Tensions escalate when a publishing company shows interest in the book, triggering a series of events that will challenge the delicate relationships between Thomas, Bea, and their animal companions. The company's marketing plan labels Peter as a troublemaker while the proposed billboard design for an upcoming film presents him in an unflattering light as the villain. Feeling crushed, Peter seeks solitude and journeys into town, where he encounters Barnabas (Lennie James), an older rabbit claiming to have known Peter's father.
As Peter and Barnabas explore the city, they unwittingly fall into the clutches of animal catchers, leading them to a pet pound overseen by the enigmatic Amelia. Barnabas appears to have ulterior motives and cunningly helps Peter escape, introducing him to a hidden lair where they indulge in stolen treats. Amidst their escapades, Barnabas shares tales of Peter's father's covert operations, revealing that he often resorted to theft to ensure his family's survival during hard times. When Thomas and Bea finally locate Peter, they find him ensnared in Barnabas’ dubious schemes.
The following morning, Peter recaps his adventures to Benjamin Bunny (Colin Moody), persuading him and the other rabbits to join Barnabas in a bold plan to rob the local farmers market of dried fruit. Simultaneously, Thomas and Bea revisit their collaboration with Nigel Basil-Jones (David Oyelowo), only to discover that his latest ideas are anything but tasteful.
As the rabbits get caught in a petting zoo during a rescue attempt, Barnabas's real agenda surfaces: he never had any connection to Peter's father and has simply been using Peter as a pawn for his gain. Faced with this betrayal, Peter decides to confront Barnabas. Recognizing the sincerity of Thomas, he seeks his help for a daring mission to rescue their captured friends. However, their initial efforts hit a snag when their truck breaks down, prompting them to consult Bea just as she is embroiled in a meeting with Nigel, who has grand but misguided plans for Peter and his comrades, leading them into outlandish escapades.
With Bea's quick thinking, she shifts her focus from Nigel's project to support Thomas and Peter, guiding them through their extraordinary adventure bent on saving their friends from despair. Eventually, Peter, Benjamin, and the sisters find a way to outsmart Barnabas by binding him and his accomplices. As fate would have it, the nearby tailor accidentally transports Barnabas and his crew away, while the rabbits return the pilfered dried fruit to the market owners. This heartwarming act leads to a joyful reunion with Thomas and Bea as they head home, marking a significant moment in Peter's transformation into a more compassionate creature open to the voices of those who genuinely care for him.
In the years that ensue, Thomas and Bea are blessed with a baby girl who names her debut book "Peter Rabbit 2: The Runaway," cherishing the adventurous legacy of her father and his loyal friends.
